-
needletail
FASTX parsing and k-mer methods
-
rust-htslib
HTSlib bindings and a high level Rust API for reading and writing BAM files
-
rust-lapper
A fast and easy interval overlap library
-
minimap2
Bindings to libminimap2
-
noodles
Bioinformatics I/O libraries
-
bio
A bioinformatics library for Rust. This library provides implementations of many algorithms and data structures that are useful for bioinformatics, but also in other fields.
-
ggetrs
Efficient querying of biological databases from the command line
-
paraseq
A minimal-copy parser for FASTA and FASTQ files built for paired parallel processing
-
lib_tsalign
A sequence-to-sequence aligner that accounts for template switches
-
seq_io
Fast FASTA, FASTQ and FASTX parsing
-
rasusa
Randomly subsample reads or alignments
-
bio-seq
Bit packed and well-typed biological sequences
-
biov
A uv-style tool manager for bioinformatics: reproducible Docker-backed tools with digest-pinned lockfiles (installs as
bv) -
bio_files
Save and load common biology file formats
-
trim-galore
Fast adapter and quality trimming for NGS data — Oxidized Edition
-
biors
Command-line tools for bio-rs biological AI model input workflows
-
simd-minimizers
A SIMD-accelerated library to compute random minimizers
-
crankshaft
A headless task execution engine that supports local, cloud, and HPC
-
lightmotif
A lightweight platform-accelerated library for biological motif scanning using position weight matrices
-
grepq
quickly filter fastq files
-
alevin-fry
A suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data
-
fastLowess
High-performance LOWESS (Locally Weighted Scatterplot Smoothing)
-
fastobo
Faultless AST for Open Biomedical Ontologies
-
salti
A modern, fast, multiple sequence alignment browser - built for the terminal
-
thirdkind
Read phylogenetic tree(s) in newick, phyloXML or recPhyloXML file and build a svg representation of the tree(s) allowing 1, 2 or 3 reconciliation levels
-
atg
Convert transcripts between different file formats
-
rustqc
Fast RNA-seq QC in a single pass: dupRadar, featureCounts, 8 RSeQC tools, preseq, samtools stats, and Qualimap — reimplemented in Rust
-
eVaiutilities
variant analyzer for human genomics
-
nuclease
Streaming FASTQ preprocessor with a focus on extensibility
-
ghcli
A terminal UI for GitHub
-
bqtools
A command-line tool for interacting with BINSEQ file formats
-
sassy
Approximate string matching using SIMD
-
peacoqc-cli
Command-line tool for PeacoQC flow cytometry quality control
-
ldsc
LD Score Regression — fast Rust reimplementation of Bulik-Sullivan et al. LDSC
-
zoe
A nightly library for viral genomics
-
liquidqc
cfRNA QC + fragmentomics in a single BAM pass. Forked from seqeralabs/RustQC; extends with end-motif k-mers, soft-clip k-mers, fragment-length periodicity, per-gene Tier-2 features…
-
bed-reader
Read and write the PLINK BED format, simply and efficiently
-
rust-sasa
RustSASA is a Rust library for computing the absolute solvent accessible surface area (ASA/SASA) of each atom in a given protein structure using the Shrake-Rupley algorithm
-
kuva
Scientific plotting library in Rust with various backends
-
fqkit
cross-platform program for fastq file manipulation
-
predictosaurus
Uncertainty aware haplotype based genomic variant effect prediction
-
alignoth
creating alignment plots from bam files
-
align-cli
A command line interface for easily aligning sequences
-
lrge
Genome size estimation from long read overlaps
-
riker-ngs
Fast Rust CLI toolkit for sequencing QC metrics
-
vareffect
Variant consequence prediction and HGVS notation, concordant with Ensembl VEP
-
finch
min-wise independent permutation locality sensitive hashing ('MinHashing') for genomic data and command-line utility for manipulation
-
orphos-cli
Command-line interface for Orphos, a tool for finding protein-coding genes in microbial genomes
-
plascad
PlasCAD
-
gsearch
genome classification, probminhash hnsw, genome search
-
htsget-search
The primary mechanism by which htsget-rs interacts with, and processes bioinformatics files. It does this by using noodles to query files and their indices.
-
ontolius
A fast and safe crate for working with biomedical ontologies
-
ragc-cli
Command-line interface for the ragc AGC genome compression tool
-
fg-mako
Fast SAM/BAM sorter (installs the
makobinary) -
oarfish
A fast, accurate and versatile tool for long-read transcript quantification
-
gtars
Performance critical tools for genomic interval analysis
-
oxo-flow-cli
CLI for the oxo-flow bioinformatics pipeline engine
-
perbase
Fast and correct perbase BAM/CRAM analysis
-
fastdedup
A fast and memory-efficient FASTX PCR deduplication tool
-
orfm
A pure-Rust port of OrfM - a simple and not slow open reading frame (ORF) caller
-
fastx
reads Fasta and FastQ files with little overhead
-
merkurio
Quick k-mer-based FASTA/FASTQ sequence record extraction, and SAM/BAM record filtering plus file annotation with k-mer tags
-
mutare
simulate and analyze a stochastic agent-based model of adaptation in uncertain environments
-
vcfkit-cli
Fast VCF toolkit (normalize, liftover, filter) — validated against bcftools, built on noodles
-
read-structure
parsing and working with read structure descriptions
-
voronota-ltr
Voronota-LT is an alternative version of Voronota for constructing tessellation-derived atomic contact areas and volumes
-
hmmer-pure-rs
Pure Rust port of HMMER 3.4 — biological sequence analysis using profile HMMs
-
bitnuc
efficient nucleotide sequence manipulation using 2-bit and 4-bit encodings
-
kira-spatial
Deterministic orchestrator for spatial transcriptomics: IO, field transforms, core math, and 3D export
-
rustyms
handle proteomic mass spectrometry data and match peptides to spectra
-
anndata-memory
Thread-safe AnnData-like structure for single-cell genomics data in Rust. Provides controlled mutability, efficient memory management, and flexible data manipulation. Ideal for concurrent bioinformatics applications.
-
glurep
CLI utility for generating pdf reports from glucose readings in supported csv formats
-
kun_peng
Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all
-
rumina
High-throughput UMI-aware deduplication of next-generation sequencing data
-
primerpincer
A CLI primer trimming tool for long-read sequencing data
-
gapsmith-cli
Command-line interface for gapsmith
-
seqsizzle
A pager for viewing FASTQ and FASTA files with fuzzy matching, allowing different adaptors to be colored differently
-
modtector
A high-performance modification detection tool in Rust
-
rustybam
bioinformatics toolkit in rust
-
dreid-pack
high-performance, pure Rust library and CLI for full-atom protein side-chain packing using the DREIDING force field, Goldstein+Split DEE, and tree-decomposition DP—with native protein-ligand…
-
grit-genomics
GRIT: Genomic Range Interval Toolkit - high-performance genomic interval operations
-
intspan
Command line tools for IntSpan related bioinformatics operations
-
jam-rs
Just another (genomic) minhash (Jam) implementation in Rust
-
umi-tools-rs
A fast drop-in replacement for UMI-tools, written in Rust
-
sufr
Parallel Construction of Suffix Arrays in Rust
-
rsomics-fastq-trim
FASTQ adapter / poly-G / poly-X / fixed-length trimming. Rust port of fastp's trim hot path with rayon-parallel SE + PE pipelines and AI-friendly --json output.
-
bed2gtf
A fast and memory efficient BED to GTF/GFF converter
-
bamnado
Tools and utilities for manipulation of BAM files for unusual use cases. e.g. single cell, MCC
-
nucs
working with nucleotide and amino acid sequences
-
motif-bridge
Cross-language toolkit for converting motifs between MEME and HOMER formats
-
biometal
ARM-native bioinformatics library with streaming architecture and evidence-based optimization
-
kractor
Extract reads from a FASTQ file based on taxonomic classification via Kraken2
-
kam-pathfind
De Bruijn graph construction and variant path walking
-
compact-genome
Representation of genomes
-
rustygal
Prokaryotic Dynamic Programming Genefinding Algorithm (Rust reimplementation of prodigal)
-
sigalign
A Similarity-Guided Alignment Algorithm
-
ecgtoolkit
ECG Conversion Toolkit - read, write, and convert electrocardiogram files
-
wdl-grammar
A parse tree for Workflow Description Language (WDL) documents
-
autonomic-core
Core types, traits, and errors for the Autonomic homeostasis controller
-
rasayan
— biochemistry engine: enzyme kinetics, metabolic pathways, signal transduction, protein structure, membrane transport
-
mzdeisotope
deisotope and charge state deconvolve mass spectra
-
rapidtrees
Fast pairwise tree distance calculations (Robinson-Foulds, Weighted RF, Kuhner-Felsenstein) for phylogenetic trees
-
xpclrs
A high-performance rust implementation of the XP-CLR method
-
hgvs-weaver
High-performance HGVS variant mapping and validation engine
-
oxbow
Read conventional genomic file formats as data frames and more via Apache Arrow
-
chromsize
just get your chrom sizes
-
seqa_core
Object store support for vcf, bam, fasta, bigwig, bigbed, gff, bed, bedgraph, gtf
-
nwr
**N**CBI taxonomy and assembly **WR**angler
-
helicase
SIMD-accelerated library for FASTA/FASTQ parsing and bitpacking
-
omicsx
SIMD-accelerated sequence alignment and bioinformatics analysis for petabyte-scale genomic data
-
fasten
A set of scripts to run basic analysis on fastq files
-
gdock
Information-driven protein-protein docking using a genetic algorithm
-
deacon
Accelerated DNA sequence search and [host] depletion using minimizers
-
simdna
High-performance SIMD-accelerated DNA sequence encoding supporting all IUPAC nucleotide codes
-
iirs
Inverted repeats finder
-
chelae
A toolkit for trimming and filtering FASTQ reads
-
block-aligner
SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm
-
genomicframe-core
High-performance genomics I/O and interoperability layer
-
edf-rs
Pure Rust implementation of a reader and writer for EDF/EDF+ (European Data Format) files
-
flow-fcs
High-level Flow Cytometry Standard (FCS) file struct and operations
-
librna-sys
Low-level bindings for the ViennaRNA library
-
bbnorm-rs
BBTools BBNorm-style read depth normalization
-
primer_demux
A high-performance tool for demultiplexing sequencing reads based on primer sequences using Myers algorithm
-
parasail-rs
Rust bindings and wrapper for parasail, a SIMD C library for pairwise sequence alignment
-
libsais-rs
Rust translation of libsais for suffix array construction and related transforms
-
feagi-structures
The most core library, defines the basic data types used by FEAGI, as well as some processors to modify them
-
vcfilter
human genomics
-
biodex
Terminal-native species atlas with cached images, range maps, and taxonomy browsing
-
oxo-call
Model-intelligent orchestration for CLI bioinformatics — call any tool with LLM intelligence
-
ome_zarr_metadata
OME-Zarr (previously OME-NGFF) metadata
-
phylo
An extensible Phylogenetics library written in rust
-
dynamics
Molecular dynamics
-
coitrees
A very fast data structure for overlap queries on sets of intervals
-
gtf_splice_index
A fast, splice-aware index for GTF/GFF annotations enabling efficient transcript and gene lookup for RNA-seq read mapping and quantification
-
noodles-vcf
Variant Call Format (VCF) reader and writer
-
gen
A sequence graph and version control system
-
rtemis-a3
A3 (Amino Acid Annotation) format — parse, validate, and inspect A3 JSON files
-
seed_chain
A seeding and generic chaining mechanism for sequence-to-sequence alignment
-
reindeer2
k-mer quantification in large collections of samples
-
nexcore-homeostasis-primitives
Shared types and math for the Homeostasis Machine — biological self-regulation for software
-
microBioRust
Microbiology friendly bioinformatics Rust functions
-
rustynetics
A high-performance genomics libary specialized in handling BAM and BigWig files
-
spiking_neural_networks
A package for designing and simulating biological neural network dynamics with neurotransmission
-
rosella
Metagenome assembled genome recovery from metagenomes using UMAP and HDBSCAN
-
fastobo-owl
OWL language mapping for ontologies in the OBO flat file format 1.4
-
rust-bio-tools
A set of fast and robust command line utilities for bioinformatics tasks based on Rust-Bio
-
webgestalt
CLI for computing enrichment for different analytes using ORA, GSEA, or NTA
-
lash-rs
Genome/Metagenome sketching via, HyperLogLog, HyperMinHash and UltraLogLog
-
ontology-registry
that lets you download, store and register ontologies
-
cardio-rs
computing heart rate variability (HRV) metrics from ECG and PPG data
-
bsalign
Rust bindings for the bsalign C library
-
sourmash
tools for comparing biological sequences with k-mer sketches
-
immunum
Fast antibody and T-cell receptor numbering in Rust and Python
-
genemancer
Rust CLI toolkit for niche optimized genomics file processing and target-based variant workflows
-
wdl-format
Formatting of WDL (Workflow Description Language) documents
-
fasta-filter
Filter a (multi-sequence) FASTA file and output a subset of the records on STDOUT
-
taxonomy
Routines for loading, saving, and manipulating taxonomic trees
-
geo-soft-rs
Parser for NCBI GEO SOFT format → Arrow RecordBatches
-
kira-organelle
Deterministic aggregation and orchestration for the Kira organelle QC stack
-
twitcher
Find template switch mutations in genomic data
-
m-system
Lindenmayer system (L-system) modeling crate for developmental biology simulations
-
hamming-resonate
Fast nearest-neighbour search over fixed-length DNA sequences using Hamming distance
-
pdbtbx
open/edit/save (crystallographic) Protein Data Bank (PDB) and mmCIF files
-
pdbrust
A comprehensive Rust library for parsing and analyzing Protein Data Bank (PDB) files
-
exon
A platform for scientific data processing and analysis
-
odgi-ffi
A safe, ergonomic Rust wrapper for the odgi pangenome graph tool
-
rype
High-performance genomic sequence classification using minimizer-based k-mer sketching in RY space
-
seal
Needleman-Wunsch & Smith-Waterman sequence alignment
-
rvdna
— AI-native genomic analysis. 20-SNP biomarker risk scoring, streaming anomaly detection, 64-dim profile vectors, 23andMe genotyping, CYP2D6/CYP2C19 pharmacogenomics, variant calling…
-
sequintools
A suite of tools for manipulating and reporting on NGS data that has sequins added to the sample
-
seqkmer
High-performance FASTA/FASTQ IO and minimizer-based k-mer analysis utilities for Rust bioinformatics pipelines
-
ozx
A CLI for creating OZX archives from OME-Zarr data
-
cosmolkit
Rust-native cheminformatics and structural biology toolkit for molecules, SMILES, SDF, molecular graphs, conformers, and AI-ready workflows
-
longcallR
SNP calling and haplotype phasing with long RNA-seq reads
-
hashrope-bio
Computational biology applications of hashrope — drug resistance panels, gene-level change detection, genomic region queries, tandem repeat analysis
-
deepbiop
Deep Learning Processing Library for Biological Data
-
onelib
ONEcode file format
-
cfdnalab
Ultra-fast command-line tools for cell-free DNA fragmentomics analysis
-
wham
weighted histogram analysis method
-
cinnamon
A type-safe Nightscout client for Rust, aiming to simplify the interactions with the confusing Nightscout API
-
stela-int-to-str
Fast integer to string conversion utilities optimized for high-throughput data processing
-
cgkitten
Convert mmCIF/PDB protein structures to coarse-grained representation with Monte Carlo titration
-
biovault
A bioinformatics data vault CLI tool
-
fgumi
High-performance tools for UMI-tagged sequencing data: extraction, grouping, and consensus calling
-
igv-core
Pure async data layer for igv-rs: regions, source traits, alignment expansion, coverage, render thresholds. UI-free.
-
fasterp
High-performance FASTQ preprocessing tool - often faster than fastp with the same interface
-
crispr_screen
A fast and configurable differential expression analysis tool for CRISPR screens
-
perestroika
genetic algorithms
-
dnacomb
Count the occurances of structured sequence reads and compare to an expected library
-
oxagorn
reimplemented ARAGORN, tRNA and tmRNA detection, for bactars annotator
-
equiconc
Equilibrium concentration solver
-
lowess
(Locally Weighted Scatterplot Smoothing)
-
serrf
Systematic Error Removal using Random Forests (SERRF) normalization for metabolomics data
-
bio-forge
A pure Rust library and CLI for the automated repair, preparation, and topology construction of biological macromolecules
-
light_phylogeny
Methods and functions for phylogeny
-
nohuman
Remove human reads from a sequencing run
-
fastq-fix-i5
Rewrite FASTQ headers by reverse-complementing only the i5 (P5/index2) part in ...:i7+i5
-
axicor-node
Axicor SNN engine — BSP-lockstep orchestrator, UDP fast-path server, Night Phase daemon
-
check_build
verify a VCF file against hg19 and hg38 references using a streaming, low-memory approach
-
infer_sex
A high-performance, zero-dependency Rust library for inferring sex from variant data
-
thaf
Extracts transcript sequences and gene maps from genome FASTA files using GFF3 annotations
-
libsais
Bindings to the C library libsais for suffix array construction
-
sview-fmindex
FM-index library with slice view architecture for efficient text indexing and pattern matching
-
cyanea-phylo
Phylogenetics and trees for the Cyanea bioinformatics ecosystem
-
packed-seq
Constructing and iterating packed DNA sequences using SIMD
-
seqtkrs
reimplementation of seqtk, a fast and lightweight tool for processing biological sequences in FASTA/FASTQ format
-
faimm
Random access to indexed fasta using a mmapped file
-
data-protocol-validator
Rust validator for Data Protocol schemas - validates versioned bioinformatics analysis output against JSON Schema-based protocol definitions
-
european-data-format
European Data Format (EDF/EDF+) utilities to read and write EDF files, EDF+ files, XML files, JSON files
-
pombase-gocam
Parser for Gene Ontology Consortium GO-CAM files
-
gffx
An ultra-fast and memory-efficient toolkit for querying GFF files, written with Rust
-
rnadraw
RNA secondary structure SVG renderer CLI
-
nj
Neighbor-Joining phylogenetic tree inference. Auto-detects DNA/protein, supports multiple substitution models and bootstrap.
-
redicat
RNA Editing Cellular Assessment Toolkit: A highly parallelized utility for analyzing RNA editing events in single-cell RNA-seq data
-
ewald
SPME force calculations
-
prodigal-rs
Prokaryotic gene prediction — Prodigal rewritten in Rust
-
rsomics-seqio
Fast FASTQ reader for the rsomics-* tool family: decode-only producer thread + parallel parse, ISA-L igzip gz backend on Linux and a pure-Rust decoder elsewhere. Layer A primitive.
-
pod5lib
Pure Rust library for reading and writing POD5 nanopore sequencing files
-
tgv
Explore genomes in the terminal. Light, blazing fast 🚀, vim-motion.
-
oxo-flow-web
Web interface for the oxo-flow bioinformatics pipeline engine
-
fragtk
Fragment file toolkit
-
noodles-csi
Coordinate-sorted index (CSI) format reader and writer
-
ARGenus
ARG detection and genus-level classification using flanking sequence analysis
-
rdkit
High level RDKit functionality for rust
-
xloci
get sequences from 2bit/fa using bed/gtf/gff
-
biors-backend-candle
Optional Candle backend adapter for bio-rs runtime execution contracts
-
feagi-npu-burst-engine
High-performance burst engine for FEAGI neural processing
-
genotype_lang_core_tree
Genotype language target crate
-
flow-gate
Facade crate for flow-gate with compliance runner and benchmark binaries
-
nanalogue
BAM/Mod BAM parsing and analysis tool with a single-molecule focus
-
cuda-assembler
Two-pass text-to-bytecode assembler
-
piscem
Fast, space-efficient k-mer-based read mapper for bulk RNA-seq, scRNA-seq, and scATAC-seq
-
orthanc_sdk
Orthanc plugin SDK
-
sbol-genbank
GenBank → SBOL 3 importer for the sbol-rs ecosystem. Parses GenBank flat-file records via gb-io and emits native sbol::Document objects.
-
simpleaf
framework to make using alevin-fry and alevin-fry-ATAC even simpler
-
ferro-hgvs
HGVS variant normalizer - part of the ferro bioinformatics toolkit
-
haddock-restraints
Generate restraints to be used in HADDOCK
-
varlociraptor
calling of genomic variants using a latent variable model
-
fibertools-rs
Fiber-seq toolkit in rust
-
pairassembler
The fastest and (laptop-)friendliest paired read merger in the west
-
jseqio
Reading and writing biological sequences in FASTA or FASTQ format
-
fastqc-rust
rewrite of FastQC - a quality control tool for high throughput sequence data
-
peprs
PEP (Portable Encapsulated Projects) specification for biological sample metadata
-
nail
alignment inference tool
-
biotools
bioinformatics CLI tools for sequence analysis and manipulation
-
burn_dragon_kernel
Fused GPU kernel crate for burn_dragon execution paths
-
filterx
A command line tool to filter data by using python-like syntax
-
invariant-biosynthesis
Biosynthesis safety engine for Invariant: synthesis bundles, D/P/C invariants, hazard screening, attestation. As of 0.2.0 this crate ships from the unified Invariant workspace at https://github…
-
gb-io
parsing, writing and manipulating Genbank sequence files
-
hashfasta
Very quickly compute hashes for FASTA/FASTQ files considering only the sequence content
-
bsxplorer2
A high-performance library for bisulfite sequencing data analysis and DNA methylation research
-
klassify
Classify chimeric reads based on unique kmer contents
-
diced
reimplementation of the MinCED algorithm for identifying CRISPRs in full or assembled genomes
-
barbell
Extremely fast and accurate Nanopore demultiplexing
-
fastqgen
Random paired fastq file generation. Nothing more, nothing less.
-
exon-bigwig
Subcrate of the
exoncrate for working with BigWig files -
rusty-dna
Normalize consumer DNA genotype exports into structured SNP data via provider-specific parsers
-
securiety
parsing and validating CURIE IDs
-
coprosize
coprolite research (paleontology and archaeology): estimate the producer's body mass based on coprolite diameter by the use of regression models
-
ugv
Ultra-fast genome viewer for interactive exploration of genomic data
-
seqtui
Fast TUI toolkit for viewing, translating, and manipulating biological sequences
-
bijux-atlas
Genomics runtime for GFF3/FASTA ingest, immutable dataset artifacts, gene-query APIs, and OpenAPI export
-
rnapkin
CLI utility for drawing RNA secondary structure
-
bamslice
Extract byte ranges from BAM files and convert to interleaved FASTQ format for parallel processing
-
tinyhgvs
Lightweight Rust library for parsing HGVS variants
-
vcf-arrow
A VCF data parser using Appache Arrow as standard format
-
pbzarr
A Zarr v3 convention for per-base resolution genomic data
-
mbf-fastq-processor
The fast, reliable multitool of FASTQ processing
-
pairsnp-rs
Calculate pairwise SNP distances given a multiple sequence alignment
-
kmerutils
Kmer counting, hashing, sequence sketching
-
righor
creates model of Ig/TCR sequences from sequencing data
-
termal-msa
A viewer of multiple sequence alignments, with a text user interface
-
covar
Calls physically-linked mutation clusters from wastewater amplicon sequencing data
-
omics
Foundations for omics analysis using Rust
-
gsem
Genomic Structural Equation Modeling from GWAS summary statistics
-
orphos-core
Core library for Orphos, a tool for finding protein-coding genes in microbial genomes
-
xcorrrs
Reimplmenmentation of Comet's xcorr algorithm
-
seqwish
A variation graph inducer - build pangenome graphs from pairwise alignments
-
gsem-ldsc
LD Score Regression engine with block jackknife for genetic covariance estimation
-
verify-same-kmer-content
Verify that an SPSS has the same kmer content as a set of unitigs
-
dihardts_omicstools
Collection of different omic tools, structs and enums
-
mehari
Variant effect prediction all in Rust
-
kmerust
A fast, parallel k-mer counter for DNA sequences in FASTA and FASTQ files
-
gtars-cli
Performance critical tools for genomic interval analysis. This is the CLI
-
genedex
A small and fast FM-Index implementation
-
feagi-services
FEAGI Service Layer - Stable application boundary for transport adapters
-
matchbox-cli
A flexible processor for sequencing reads
-
genovo
Determine genes with significantly more mutations than expected by chance
-
gfatk
command line tool for manipulating small to medium sized GFA files, and specifically for output from the genome assembler MBG
-
consalifold
Consensus Secondary Structure Predictor Engaging Structural Alignment-based Error Correction
-
skope
Accelerated genome containment and abundance estimation
-
pure-onnx-ocr-sync
【Sync Version】Pure Rust OCR pipeline that runs PaddleOCR DBNet + SVTR ONNX models without C/C++ dependencies
-
tsg
Deep Learning Processing Library for Biological Data
-
parfait-gfa
gfa v1/v2 parser and validator
-
glurep-gui
GUI utility for generating pdf reports from glucose readings in supported csv formats
-
dreid-forge
A pure Rust library and CLI that automates DREIDING force field parameterization by orchestrating structure repair, topology perception, and charge calculation for both biological and chemical systems
-
htsgetr
htsget protocol server implementation in Rust
-
shadowing
example crate
-
chemical_elements
representing chemical compositions and generating isotopic patterns
-
coverm
Read coverage calculator for metagenomics
-
selexqc
High-performance parallel RNA Capture-SELEX library quality control
-
cyanea-chem
Chemistry and small molecules for the Cyanea bioinformatics ecosystem
-
tokenizations
alignments library
-
wdl-lsp
Language Server Protocol implementation for WDL
-
ska
Split k-mer analysis
-
nexwick
Parser for Nexus files and Newick strings
-
cigar_collapser
A program that collapses CIGAR strings from SAM/BAM files into shorter human-readable string
-
flow-fcs-compress
Compression codecs for flow cytometry data, tuned for FCS-format event tables
-
k2tools
Rust CLI toolkit for working with kraken2 outputs
-
mm2
minimap2 frontend
-
neuralkit
neural network toolkit / building blocks for neural networks in Rust
-
kam-index
K-mer indexing with molecule-level evidence tracking
-
tikhonov-cli
CLI for Harmony2 single-cell integration; reads .h5ad, writes .h5ad + Patikas-schema JSON
-
minimap2-temp
Bindings to libminimap2
-
scidataflow
A command-line tool to manage scientific research project data
-
holodeck
Modern NGS read simulator
-
snp-index
Fast SNP indexing and read matching with scdata integration (cell × SNP sparse matrices)
-
gapsmith-db
Loaders for gapseq's reference data tables (SEED, MNXref, biomass JSON, pathway tables)
-
windchime
Allen Lab QIIME2 pipeline
-
biopath
Shortest paths in biological overlap graphs with or without indexing
-
tsalign
A sequence-to-sequence aligner that accounts for template switches
-
pluma-plugin-trait
A trait defining the plugin interface for PluMA (Plugin-based Microbiome Analysis)
-
barcode-count
NGS barcode counter for DEL, CRISPR-seq, and Barcode-seq
-
sequenceprofiler
sequence similarity based on identity kmers and all sequence profiling under one rust crate
-
pubmeddb
PubMed query tool (Rust core)
-
plato-genepool-tile
PLATO cognitive architecture component
-
axicor-core
Axicor SNN engine — C-ABI memory contracts, SoA layouts, and IPC primitives
-
ibu
high throughput binary encoding genomic sequences
-
convert_genome
Convert DTC, VCF, or BCF genome files to VCF, BCF, or PLINK 1.9
-
bigsig
Large-scale Sequence Search with BItsliced Genomic Signature Index (BIGSIG)
-
yacrd
Using all-against-all read mapping, yacrd performs: computation of pile-up coverage for each read and detection of chimeras
-
kira-nuclearqc
Deterministic CLI for nuclear state and transcriptional plasticity analysis from 10x scRNA-seq MTX inputs
-
fuzzyfold
Nucleic acid secondary structure kinetics
-
vcf-reformatter
Fast VCF file parser and reformatter with VEP and SnpEff annotation support which can output to MAF
-
blobtk
Core utilities for BlobToolKit
-
genomic-system-finder-hmm
Pure Rust HMMER3-compatible profile HMM search engine for protein sequences
-
transcriptomic-rs
Expression matrix assembly and normalization → Arrow RecordBatches
-
kraken2-pure-rs
Taxonomic sequence classification system — Rust port of Kraken 2
-
genebears
Lightweight Rust client for the GeneBe genetic variant annotation API with DuckDB caching and rate limiting
-
biodivine-pbn-control
controlling parametrized Boolean networks
-
bv-conformance
Conformance test runner for bv-registry manifests
-
aardvark-bio
Aardvark - A tool for sniffing out the differences in vari-Ants
-
genome-sh
The jq of genomics. Fast, local, human-readable variant analysis.
-
cliproc
A fast, low-level, and configurable command-line processor
-
cyanea-align
Sequence alignment algorithms for the Cyanea bioinformatics ecosystem
-
minimap2-sys
Bindings to libminimap2
-
bv-types
Typed I/O vocabulary for bv manifests
-
repeatmasker-rs
Fast Rust postprocessing and masking for RepeatMasker .out/.cat annotations
-
prseq
Rust tools (with Python bindings) for sequence analysis
-
ggca
Computes efficiently the correlation (Pearson, Spearman or Kendall) and the p-value (two-sided) between all the pairs from two datasets
-
rsomics-fasta-stats
Per-record statistics for FASTA files (num_seqs, sum_len, GC%, N50, …) — Rust port of
seqkit stats(FASTA-only subset) -
bamrescue
check Binary Sequence Alignment / Map (BAM) files for corruption and repair them
-
vcfkit-core
Core library for vcfkit: VCF normalize, liftover, and filter operations
-
gen-capnp-schemas
Shared Cap'n Proto schemas and generated Rust modules for Gen crates
-
refman
A command-line manager for bespoke reference datasets used in bioinformatic analyses
-
genepred
port for the GenePred format in Rust
-
viguno
Phenotype/disease for VarFish
-
piscem-rs
piscem with semantic parity harness
-
numpress-rs
A pure rust implementation of ms-numpress, a fast, minimally lossy compression algorithm for mass spectrometry data
-
genomemask
mask specific regions of a genome in any format
-
rustkmer
High-performance k-mer counting tool in Rust
-
noodles-sam
Sequence Alignment/Map (SAM) format reader and writer
-
biosynth
CLI: synthetic data generator for BioVault
-
d4-hts
The htslib binding used by D4
-
fastars
Ultra-fast QC and trimming for short and long reads
-
nthash
rolling hash function for hashing all possible k-mers in a DNA sequence
-
chemp
chemical formulas parser
-
placecare
A toolkit to quickly search for cis-acting regulatory elements using the PLACE database
-
vareffect-cli
CLI for vareffect — annotate genomic variants without Ensembl VEP
-
galah
Microbial genome dereplicator
-
raxtax
k-mer-based non-Bayesian Taxonomic Classifier
-
orthanq
quantify haplotypes in an uncertainty-aware manner
-
mini_myers
SIMD myers for short queries
-
msafara
View, edit, and explore multiple sequence alignments in your terminal
-
smyl
Artificial Neuronal Network in Rust
-
use-bioinformatics
Facade crate for primitive RustUse bioinformatics vocabulary
-
multiseqex
Multi-sequence extractor from FASTA using FAI indexing, with parallelism and flexible region input formats
-
fastax
Make phylogenetic trees and lineages from the NCBI Taxonomy database
-
fastlin
an ultra-fast program for MTBC lineage typing
-
ncbitaxonomy
Read NCBI Taxonomy Database from files and work with NCBI Taxonomy DB
-
sampaint
A colouriser for the SAM/BAM file format
-
fmlrc
FM-index Long Read Corrector - Rust implementation
-
pillar-bio
Columnar file format for multi-experiment genomic signal data
-
electrocardiogram-synthetic-data-generator
Electrocardiogram synthetic data generator Rust crate. Work in progress. Do not use in production. AI-generated code. This is port of work by PierreElias/IntroECG.
-
loess-rs
LOESS (Locally Estimated Scatterplot Smoothing) implementation in Rust
-
phenotype-forge
CLI task runner
-
papasmurf
Platform-Accelerated Package for Alignment-free SMURF analysis
-
quadrank
Fast rank over binary and size-4 DNA alphabets
-
nodedb
Local-first, real-time, edge-to-cloud hybrid database for multi-modal workloads
-
sbol-fasta
FASTA → SBOL 3 importer for the sbol-rs ecosystem. Pure-Rust, zero new transitive dependencies.
-
cealign
Combinatorial Extension (cealign) algorithm to align protein structures
-
genotype_parser
Genotype language parser crate
-
gsem-matrix
Matrix utilities for GenomicSEM: nearest positive-definite, half-vectorization, PSD smoothing
-
atglib
handle transcripts for genomics and transcriptomics
-
strobemers
A toolkit for generating strobemers
-
dabuild
Access genome build metadata
-
pileup-hi
High-throughput, extensible SAM/BAM pileup generator
-
rustome
Genetic tools
-
scattr
estimating the copy number of large tandem repeats
-
phylotree
deal with phylogenetic trees and distance matrices
-
chainfile
working with genomics chain files
-
sshash
Sparse and Skew Hashing of k-mers - Command line tool
-
stats_on_gff3_ncbi
Calculate statistics such as CDS GC3 ratio, intron GC ratio, flanking gene region GC ratio, first intron length, number of introns, CpG ratio, etc
-
gv-core
Core library for the terminal genome viewer
-
haptk
Haplotype analysis toolkit
-
mim-index
Small index enabling multithreaded fastq.gz decompression
-
extended-htslib
extended HTSlib bindings and a high level Rust API for reading and writing BAM files
-
phenotype-sentinel
Rate limiting, circuit breaker, bulkhead
-
accord-rs
Calculate consensus sequences
-
gtars-genomicdist
Rust port of GenomicDistributions: tools for computing statistics for genomic interval sets
-
crib
reading genome track files
-
rsomics-fastq-filter
FASTQ per-read quality + length filter. Rust port of fastp's quality/length filter (pass/fail whole reads; no trimming). SE and PE.
-
cuda-biology
Biological agent with instinct pipeline
-
yeast
Shell Trick
-
nucleob
bioinformatics: nucleobases and amino acids statistics
-
ebiotic
interacting with common bioinformatics web services
-
virust-splicing
High-performance command-line program for analyzing HIV-1 splicing patterns from NGS data
-
fastqc-rs
A fast quality control tool for FASTQ files written in rust
-
mikan-rs
A medical image kit for segmentation metrics evaluation, native Rust support, and Python bindings for cross-language performance
-
peprs-cli
Command-line tool for validating, inspecting, and converting PEP projects
-
na_seq
DNA, RNA, and amino acid sequence types and functions
-
phylo_grad
Fast gradient calculation of the Felsenstein algorithm with respect to the rate matrix
-
rotamer
NERF-based sidechain coordinate placement for 29 amino acid types; build.rs bakes all bond geometry as f32 literals, custom libm-free sincosf/rsqrtf, #[repr(C)] stack-only output, zero heap, no-std
-
kondrak-aline
Kondrak's ALINE alignment algorithm
-
igv-rs
Interactive terminal genome viewer for FASTA / VCF / BAM / GFF / BED / bigWig / BEDPE. Includes a bundled-igv.js browser companion.
-
ref-solver
Solve reference genome identification from BAM/SAM headers
-
mmft
A minimal fasta toolkit
-
classeq-cli
A command line interface for the classeq library
-
bammap2
A lightweight wrapper to run minimap2 (v2.30) alignments directly on BAM file
-
pheno-core
Core types and error handling for phenotype-config
-
sweepga
Efficient pangenome alignment filtering and sparsification tool
-
bam_tide
A fast and memory-efficient BAM processing toolkit for coverage calculation and quantification, designed as a scalable alternative to deeptools bamCoverage for large sequencing datasets. And additional BAM tools.
-
alphabeta
Tools for analysing epigenetic data
-
elias_fano_rust
An optimized implementation of Sebastiano Vigna's Elis-Fano quasi succint datastructure
-
opentools
toolbox that process OpenST chip data
-
gfautil
Command line tools for working with GFA files and related formats
-
rsomics-fasta-index
FASTA index (.fai) creation and random-access fetch — Rust port of samtools faidx
-
fxsplit
split FASTX into N chunks/files/headers
-
awry
creating FM-indexes from FASTA/FASTQ files. AWRY is able to search at lightning speed by leveraging SIMD vectorization and multithreading over collections of queries.
-
bio_utils_rs
bioinformatic analysis
-
genotype_lang_ts_config
Genotype language TypeScript target config crate
-
infercnasc
Copy number alteration inference from scRNA-seq data
-
bam-builder
easily building BAMs for testing
-
cyanea-omics
Omics data structures for the Cyanea bioinformatics ecosystem
-
oxo-flow-venus
Venus: Clinical-grade tumor variant detection pipeline built on oxo-flow
-
Stellerator
Extract candidate fusion-supporting reads for target genes from indexed BAM files
-
seqalign
Sequence alignment using edit operations
-
xsra
A performant and storage-efficient CLI tool to extract sequences from an SRA archive with support for FASTA, FASTQ, and BINSEQ outputs
-
efficient_pca
Principal component computation using SVD and covariance matrix trick
-
skani
fast tool for calculating ANI between metagenomic sequences, such as metagenome-assembled genomes (MAGs). It is extremely fast and is robust against incompleteness and fragmentation, giving accurate ANI estimates.
-
flow-plots
Package for drawing and interacting with plots in flow cytometry data
-
rustalign-fmindex
Ultrafast DNA sequence aligner using FM-index and Smith-Waterman
-
lightdock
Macromolecular docking software based on the GSO algorithm
-
bgzf
working with explicitly BGZF compressed data
-
kira-microenvironment
Deterministic, explainable ligand-receptor microenvironment interaction scoring for single-cell expression data
-
flash-cli
Command-line interface for the FLASH read merging algorithm
-
epimetheus-methylome
DNA motif representation and methylation analysis, supporting IUPAC codes and Nanopore methylation data (6mA, 5mC, 4mC)
-
pyanndata
Rust APIs
-
lorikeet-genome
Strain resolver and variant caller via local reassembly for metagenomics
-
finch_cli
min-wise independent permutation locality sensitive hashing ('MinHashing') for genomic data and command-line utility for manipulation
-
cyanea-ml
ML primitives for bio (embeddings, etc.) for the Cyanea bioinformatics ecosystem
-
seqx
A command-line tool for processing and analyzing biological sequences
-
biofile
reading bioinformatics related files
-
distance_aa
A backend for the distAAnce web application
-
ensemblcov
human genomics
-
granges
command line tool for genomic range operations
-
kgst
containing the implementation of a K-Truncated Generalized Suffix Tree using Ukkonen's Algorithm
-
noodles-tabix
Tabix (TBI) format reader and writer
-
rrblup-rs
R/rrBLUP package for mixed model analysis
-
hts-sys
HTSlib bindings
-
ferrolens
A terminal-first review lens for bioinformatics result tables
-
nexcore-spliceosome
Pre-translation structural expectation generator for NMD pipeline surveillance
-
stratiphy
Phenotype-driven identification of disease subgroups
-
sketchy-rs
Rust command line client for Sketchy
-
fusta
leverages the FUSE interface to transparently manipulate multiFASTA files as independent files
-
kam-call
Statistical variant calling with confidence intervals
-
peprs-eido
JSON-schema validation for PEP projects (eido extensions)
-
gtars-uniwig
uniwig: a tool for computing coverage from BED files over genomic intervals
-
RagatagSorter
sort Ragatag reads by their tags
-
gstest-kits
gstest kits
-
wdl-analysis
Analysis of Workflow Description Language (WDL) documents
-
deepbiop-cli
CLI tool for Processing Biological Data
-
d4-bigwig
The libBigWig binding used by D4
-
kira-mmcif
Low-level, streaming mmCIF parser focused on protein coordinates
-
lightmotif-py
PyO3 bindings and Python interface to the lightmotif crate
-
flowtigs
An algorithm for calculating flowtigs in a De Bruijn graph of DNA reads in metagenomes
-
gapsmith-core
Core types for gapsmith: Model, Reaction, Metabolite, StoichMatrix, GPR
-
rna-ss-params
RNA secondary structure parameters
-
genomic-system-finder-cli
Command-line interface for detecting macromolecular systems in microbial genomes
-
kraken2_rs
An ultra-fast, low-memory footprint and accurate taxonomy classifier for all
-
grumpy
Genetic analysis in Rust
-
gen-annotations
Annotation models and graph operations for Gen
-
use-residue
Primitive biological residue vocabulary for RustUse
-
cyto
Ultra high-throughput processing of 10x-flex single-cell sequencing data
-
seqtable
High-performance FASTQ sequence counter
-
kamino-cli
Build phylogenomic datasets in seconds
-
pmq
PubMed query tool (Rust core)
-
use-sequence
Primitive biological sequence vocabulary for RustUse
-
vcf
VCF Parser
-
kira-qc
FastQC-compatible QC tool written in Rust
-
codonrs
Calculate relative synonymous codon usage for coding DNA sequences in a fasta file
-
isONclust3
novel de novo clustering algorithm. isONclust3 is a tool for clustering either PacBio Iso-Seq reads, or Oxford Nanopore reads into clusters, where each cluster represents all reads that came from a gene family…
-
hyper-gen
HyperGen is a high-performance Rust library to sketch genomics files into hypervectors and realize fast Average Nucleotide Identity (ANI) approximation
-
fqgrep
Search a pair of fastq files for reads that match a given ref or alt sequence
-
ecdna-lib
The ecDNA distribution for the evolutionary of extra-chromosomal DNA (ecDNA)
-
sumi
analysis for small RNA libraries with UMIs
-
kira-shared-sc-cache
Shared deterministic binary cache reader/writer for Kira single-cell pipelines (kira-organelle.bin and expr.bin)
-
genotype_lang_py_config
Genotype language Python target config crate
-
lib3dmol
written in rust to read, manipulate, select atoms in protein structure files
-
mni2mz3
Brain imaging surface mesh file format converter
-
back_to_sequences
Back to sequences: find the origin of kmers
-
podders
Write uncompressed Pod5 files in native rust. No FFI! PODDDDERS
-
motif_finder
Find motifs using Gibbs Sampler, Median String, and Randomized Motif Search algorithms in a fasta formatted file of reads Refer to the README to understand the input data
-
mzcv
Handle controlled vocanulaires (CVs) and ontologies, both statically and dynamically
-
skesa-rs
Rust port of NCBI's SKESA genome assembler
-
aplustools
Rust port of Python 'aplustools' utility library
-
genome-graph
Representation of genome graphs
-
omics-molecule
Foundational representations of biological molecules in the Rust omics ecosystem
-
bio-streams
Streaming bioinformatics data types
-
nucleobases
low-level brick crate for managing nucleobases as data in code
-
bio-jtools
A suite of bioinformatics tools for interacting with high throughput sequencing (HTS) data
-
rsabpoa
abpoa rust binding
-
scdata
High-performance Rust library for constructing sparse single-cell UMI count data with deterministic MatrixMarket export
-
rsomics-vcf-utils
VCF utility toolkit — view, filter, count, stats, and convert operations
-
fpa_lr
fpa filter long read mapping information to save disk space
-
pluma
Plugin Interface for Rust - provides FFI bindings and utilities for writing PluMA plugins in Rust
-
deepbiop-fq
Deep Learning Preprocessing Library for Fastq Format
-
iitree-rs
Implicit augmented interval tree (IAITree/cgranges) with memory-mapped disk storage
-
fastq
A parser for fastq
-
gosh-adaptor
Adaptor for chemical model
-
seqsum
Robust sequence checksums for FASTA/FASTQ
-
axicor-baker
Axicor SNN engine — offline topology compiler. TOML brain DNA → binary .state/.axons memory dumps
-
crankshaft-engine
The core engine that comprises Crankshaft
-
toxannotator
tox annotator for ToxDB
-
libpairassembly
The fastest and (laptop-)friendliest paired read merger in the west
-
crankshaft-events
Definition of events sent by Crankshaft
-
seq-events
A minimal, zero-copy streaming parser for FASTA/FASTQ files
-
fasta_windows
Make quick statistics in windows from a fasta file
-
cyanea-stats
Statistical methods for the Cyanea bioinformatics ecosystem
-
oxo-flow-core
Core library for the oxo-flow bioinformatics pipeline engine
-
mpileup
Pile up multiple bam files site by site
-
bam2ab1
-
primer3
Safe Rust bindings to the primer3 primer design library
-
noodles-bam
Binary Alignment/Map (BAM) format reader and writer
-
gfa-reader
Reading gfa format v1
-
libparasail-sys
Unsafe Rust bindings for the parasail C library
-
use-annotation
Primitive annotation vocabulary for RustUse
-
chainsaw
manipulate newick trees
-
nafcodec
Rust coder/decoder for Nucleotide Archive Format (NAF) files
-
nthash-rs
Pure‑Rust port of ntHash
-
hooty
Direct computing of K2P min-max distance matrix
-
abpoa-rs
Rust bindings for abPOA: Adaptive Banded POA
-
rust_deseq2
A pure Rust implementation of DESeq2 for differential expression analysis of RNA-seq data
-
rsomics-fastq-stats
Per-file statistics for FASTQ files (num_seqs, sum_len, N50, GC%, Q20/Q30%, AvgQual, …) — Rust port of
seqkit stats(FASTQ) -
burn_dragon_vision
Foveation and vision sampling utilities for burn dragon
-
noodles-fasta
FASTA format reader and writer
-
biostats
A bioinformatics library
-
edlib_rs
interface to the C++ edlib library
-
fastqc-compliant-rs
translation of FastQC - quality control for high-throughput sequencing data
-
mmap-bitvec
working with bit-vectors backed by memory-mapped files
-
genomeguesser
Identifying the reference genome used for variant calling and determining whether variant positions are from a 0-based or 1-based coordinate system
-
ksw2rs
Native Rust port of ksw2 (ksw2_extz2_sse) with stable-Rust SIMD backends
-
liblrge
Genome size estimation from long read overlaps
-
xdrfile
Wrapper around the gromacs libxdrfile library. Can be used to read and write gromacs trajectories in xtc and trr format.
-
peacoqc-rs
PeacoQC quality control algorithms for flow cytometry
-
stats_on_gff3
Calculate statistics such as CDS GC3 ratio, intron GC ratio, flanking gene region GC ratio, first intron length, number of introns, CpG ratio, etc. Examples: stats_on_gff3 Homo_sapiens…
-
spillover-bio
Genomics-focused disk-spilling sort pipeline for FASTQ/FASTA sequence records
-
biotest
Generate random test data for bioinformatics
-
bsxplorer-ci
A high-performance tool for bisulfite sequencing data analysis and DNA methylation research
-
lightmotif-tfmpvalue
Rust reimplementation of TFMPvalue for the lightmotif crate
-
tf-binding-rs
Fast transcription factor binding site prediction and FASTA manipulation in Rust
-
phenotype-patch
Unified diff and patch
-
mapping_info
Compact mapping/run metrics container and reporting utilities for sequencing read mapping pipelines
-
cigar-lodhi-rs
Lodhi subsequence kernel on CIGAR strings
-
omics-coordinate
Foundational representations of coordinates in the Rust omics ecosystem
-
binseq
A high efficiency binary format for sequencing data
-
sketchlib
Genome and amino-acid sketching
-
nu_plugin_bio
Parse and manipulate common bioinformatic formats in nushell
-
tsg-cli
analyze and manipulate transcript segment graph (TSG)
-
orthanc_client_ogen
Orthanc API client library produced by OpenAPI Generator
-
obofoundry
Structures to deserialize OBO Foundry listings into
-
proteogenomics
-
ferromic
Rust-accelerated population genetics toolkit with ergonomic Python bindings
-
gskits
common kits
-
bio_apis
DNA and RNA sequence types and functions
-
genotype_lang_rs_config
Genotype language Rust target config crate
-
microbiorust-py
Python bindings for microBioRust Microbiology friendly bioinformatics Rust functions
-
nucleaze
Read filtering using k-mers
-
rsomics-gff-utils
GFF/GTF utility toolkit — count, filter, extract, sort, convert, and stats operations
-
ontime
Extract subsets of ONT (Nanopore) reads based on time
-
flow-gates
Package for drawing and interacting with gates in flow cytometry data
-
ross
A set of scripts to run basic analysis on fastq files
-
consprob
Quick Probability Inference Engine on RNA Structural Alignment
-
gtars-igd
IGD: a high-performance genomic interval search tool
-
chem-equations
parsing and balacing chemical equations
-
entrez-rs
Rust wrapper for the Entrez API
-
igv-render
Graphical (SVG / PNG) snapshot renderer for igv-rs
-
nanocov
Rust Coverage Calculator and QC Plot Generation Tool
-
bustools_cli
Rust reimplementation of bustools for scRNAseq processing
-
use-alphabet
Primitive biological alphabet vocabulary for RustUse
-
markov_genome
Learn the properties of a FASTA sequence database and simulate sequences in a Markov process
-
heme
PDB reader and other protein modeling tools
-
bird_tool_utils
Microbial genomics utility functions
-
pilercr-parser
A parser for the output of the PILER-CR CRISPR array annotation tool
-
gosh-model
Chemical model for gosh
-
seq-hash
A SIMD-accelerated library to compute hashes of DNA sequences
-
frag_gene_scan_rs
gene prediction model for short and error-prone reads
-
gecco
Gene Cluster prediction with Conditional Random Fields
-
termal-alignment
Alignment parsing and metrics for the termal multiple-sequence-alignment viewer
-
fastLoess
High-level, parallel LOESS (Locally Estimated Scatterplot Smoothing) implementation in Rust
-
convert-af
converting alevin-fry output to the AnnData format
-
psdm
Compute a pairwise SNP distance matrix from one or two alignment(s)
-
rustalign-aligner
Ultrafast DNA sequence aligner using FM-index and Smith-Waterman
-
spikeq
A synthetic FASTQ record generator with pattern spiking
-
kam-assemble
Molecule assembly from duplex UMI sequencing reads
-
seq-here
A fast tool for bio-sequence file processing
-
rsedlib
rust binding of edlib
-
dunbrack
A zero-cost Rust interface to the Dunbrack 2010 rotamer library with O(1) allocation-free lookups, bilinear interpolation, and compile-time embedded static tables for protein side-chain packing
-
libmsa
operations on multiple sequence alignments
-
pa-types
Core library types for global pairwise alignment
-
filterx_info
The builtin function documentation library for filterx
-
gapsmith-draft
Draft model construction for gapsmith (port of src/generate_GSdraft.R + helpers)
-
varforge
Synthetic cancer sequencing test data generator
-
sparc
binding
-
exon-vcf
Exon VCF
-
mzdeisotope-map
deisotope and charge state deconvolve mass spectra
-
hts
Rust binding for htslib
-
fgumi-raw-bam
Raw byte-level operations on BAM alignment records
-
use-chemical-constants
Reusable chemical and thermodynamic constants for RustUse
-
use-organ
Primitive biological organ vocabulary for RustUse
-
smafa
Read aligner for small pre-aligned sequences
-
phenotype-vessel
Container utilities
-
forgers
VCF manipulation based on FORGe ranking
-
nwbview
Neurodata Without Borders viewer
-
axicor-compute
Axicor SNN engine — dual-backend (CUDA / AMD HIP) GPU compute kernels with CPU fallback
-
pmcdb
PubMed query tool (Rust core)
-
recmap
reading and working with recombination maps in Rust
-
uniprot
Rust data structures and parser for the Uniprot database(s)
-
biors-core
Core biological sequence validation and protein tokenization contracts for bio-rs
-
xdf
Read XDF Files
-
omnitigs
Omnitig-related algorithms
-
ff_structure
fuzzyfold's secondary structure representations
-
node-to-arc-centric-dbg
Convert node-centric de Bruijn graphs as output by BCALM2 into arc-centric de Bruijn graphs as edge lists
-
rust-featurecounts
A fast feature counting tool for prokaryotic RNA-seq analysis, compatible with featureCounts
-
cyanea-gpu
GPU compute abstraction (CUDA/Metal) for the Cyanea bioinformatics ecosystem
-
rsomics-kmer
K-mer encoding, canonicalisation, ntHash rolling hash, MurmurHash3, k-mer counting for the rsomics-* tool family. Layer A primitive.
-
libnail
that performs profile Hidden Markov Model (PHMM) biological sequence alignment
-
biodiff-align
Sequence alignment bindings for biodiff
-
proteinogenic
Chemical structure generation for protein sequences as SMILES string
-
ngs
Command line tool for processing next-generation sequencing data
-
finalspark-rs
live data recording from MEA devices
-
lorikeet-rs
Strain resolver for metagenomics
-
mutexpect
functions for determining potential point mutations in a genetic sequence and their statisical probability
-
crankshaft-docker
Docker facilities for Crankshaft
-
sfasta
Better FASTA sequence compression and querying
-
seqhash
Fast mismatch-tolerant sequence lookup with disambiguation
-
tru-ols
Command-line tool for TRU-OLS flow cytometry unmixing
-
fastleng
read length statistics tool
-
kira-autolys
Deterministic, explainable autophagy/lysosome dependency QC for single-cell expression data
-
exon-bam
Exon BAM
-
syntesuite
TODO
-
protein-translate
Translate nucleotide sequence to protein
-
genotype_path
Genotype language path crate
-
gfa
working with graphs in the GFA (Graphical Fragment Assembly) format
-
cyanea-core
Shared primitives, traits, and utilities for the Cyanea bioinformatics ecosystem
-
mzcore
Core logic for handling massspectrometry in Rust
-
nanocount
A dual-guide protospacer counter for long-read nanopore data
-
rsomics-fastq-umi
FASTQ inline-UMI extract + stamp. Rust port of fastp's UMI processing — full --umi_loc set (read1/read2/index1/index2/per_index/per_read): move the UMI into the read name. SE and PE.
-
ppgg
associated executable, the library provides tools for building tools that can parse and work for VCF and FASTA files while the associated executable is a command line tool for generating…
-
cyanea-struct
Protein and nucleic acid 3D structures for the Cyanea bioinformatics ecosystem
-
d4tools
The CLI utils for D4 file format
-
rsomics-deseq-prep
Filter low-count genes and normalize a count matrix for differential expression — pre-DESeq2 prep
-
sais_drum
SAIS algorithm for suffix array construction
-
gtars-io
Small, io focused crate for gtars
-
kbo-cli
Command-line interface to the kbo local aligner
-
motif-scanner
Command line tool for scanning DNA sequences for transcription factor binding sites
-
libprosic
calling of genomic variants using a latent variable model
-
kira-simd
Shared deterministic SIMD primitives for Kira tools
-
ambigviz
Identify and plot ambiguous nucleotide bases at given positions from a BAM file
-
xch-ceb
XCH - Chemical Equation Balancer
-
use-gene
Primitive gene identity vocabulary for RustUse
-
omics-variation
Foundational representations of variation in the Rust omics ecosystem
-
bindashtree
MinHash based phylogenomics via neighbor joining
-
strif
identify interruptions in short tandem repeats across the genome
-
psylink
GUI for PsyLink neural interface for receiving/graphing biosignals and predicting user's intentions
-
kira-energetics
Deterministic, explainable energy-landscape analysis for cellular states
-
genomers
Package to download NCBI genome data and metadata
-
libradicl
support library for alevin-fry
-
sgcount
A fast and flexible sgRNA counter
-
genotype_lang_rs_project
Genotype language Rust target project crate
-
phenopacket-builder
Streamline programmatic assembly of Phenopacket Schema building blocks
-
noodles-cram
CRAM format reader and writer
-
poasta
Fast, optimal, gap-affine partial order alignment
-
smiles-parser
SMILES (chemical formula) parser based on the OpenSMILES spec
-
tiny-dict
Fast hashbrown-based k-mer dictionary for small references (drop-in alternative to sshash)
-
bustools
Interacting with the kallisto/bus format of scRNAseq data
-
deepbiop-fa
Deep Learning Preprocessing Library for Fastq Format
-
circos-rs
Circos - circular data visualization, ported from Perl to Rust
-
consalign
RNA Structural Aligner Based on Transfer-learning and Thermodynamic Ensemble Model
-
ragc-core
Core compression and decompression algorithms for the AGC genome compression format
-
cyanea-seq
Sequence I/O and manipulation for the Cyanea bioinformatics ecosystem
-
rsomics-fastqc
Per-file FASTQ quality-control report (FastQC-equivalent: per-base quality, GC, N, length, duplication, overrepresented, adapter, k-mer) — independent Rust reimplementation, MultiQC-parseable output
-
kira-biodata-manager
Reproducible bio-data manager with a project-local store and a shared global cache. kira-bm it's like npm/cargo/pip for bioinformatics.
-
gapsmith-align
Alignment abstraction for gapsmith: blast/diamond/mmseqs2 runners + precomputed TSV ingestion
-
bamsalvage
Rust version of bamsalvage, retrieving sequences from a corrupted BAM file as much as possible
-
filterx_source
The source library for filterx
-
lib_xch
xch-ceb's official lib
-
CAGrepeat-analyzer
CAG repeat for human genomics
-
sigalign-utils
utils for core
-
fgumi-consensus
Consensus calling algorithms for fgumi: simplex, duplex, and CODEC
-
simd-sketch
A SIMD-accelerated library to compute a b-bit bottom-h sketch
-
use-trait
Primitive biological trait and phenotype vocabulary for RustUse
-
ff_energy
fuzzyfold's nearest neighbor free energy evaluations
-
genomap
A small library for storing generic genomic data indexed by a chromosome
-
mzdeisotoper
Deisotoping and charge state deconvolution of mass spectrometry files
-
rustalign-cli
Ultrafast DNA sequence aligner using FM-index and Smith-Waterman
-
rsomics-sample-sheet
Parse, validate, and convert sample sheets (Illumina/custom TSV) — check FASTQ paths, detect paired-end, generate configs
-
rsomics-intervals
BED algebra + interval index + GFF/GTF interval extraction for the rsomics-* tool family. Layer A primitive.
-
pattern_partition_prediction
Reading and querying k-mer pattern partition information
-
diced-py
PyO3 bindings and Python interface to the diced crate
-
rumi
PCR Deduplication via directional adjacency
-
give_a_sheet
Toolkit for generating input samplesheets for a variety of nf-core pipelines
-
dgcount
Dual guide CRISPR counter
-
drprg
Drug resistance prediction with reference graphs
-
refget-server
Axum-based GA4GH refget Sequences v2.0.0 and Sequence Collections v1.0.0 server
-
orthanc_api
Orthanc API hand-written response models
-
gfastats
GFA statistics
-
seqtk-rs
sequence processing tool written in Rust for manipulating FASTA/FASTQ files. Pure rust version of seqtk.
-
igv-serve
Local HTTP server that mirrors the igv-rs TUI's view in igv.js
-
bacdive
analyzer for microbial genomics
-
kbo
Local alignment search with k-bounded matching statistics
-
strobemers-rs
strobemers
-
rsomics-pdb-chain
Extract or split PDB chains — list, extract single chain, or split all into separate files
-
rsomics-motif-scan
Scan FASTA sequences for IUPAC DNA motif occurrences — BED output of match positions
-
noodles-util
noodles support utilities
-
kam-bio
Alignment-free variant detection for duplex UMI sequencing
-
fg-sra
High-performance SRA-to-SAM/BAM converter replacing NCBI sam-dump
-
scidb
PubMed query tool (Rust core)
-
rsomics-fastq-correct
FASTQ k-mer-spectrum substitution-error correction. Independent Rust port of BFC (lh3): trusted-k-mer threshold + best-first correction walk. SE and PE.
-
rsomics-cell-filter
Filter cells by QC metrics — min genes, min UMIs, max mito fraction from a barcode stats TSV
-
libsfasta
Better FASTA sequence compression and querying
-
tsg-btsg
analyze and manipulate transcript segment graph (TSG)
-
exon-io
IO utilities for Exon
-
onecode
Rust bindings for ONEcode - a data representation format for genomic data
-
edit_tree
Edit trees in rust
-
data_table
A lightweight Rust data table structure supporting numeric columns and categorical factors
-
rsomics-vcf-filter
VCF/BCF record filtering by region, quality, INFO/FORMAT fields — Rust port of bcftools view/filter
-
saboten
biedged graphs, cactus graphs and trees, and an algorithm for finding ultrabubbles in variation graphs
-
genomic-system-finder-core
Core library for detecting macromolecular systems in microbial genomes
-
noodles-bed
BED (Browser Extensible Data) reader and writer
-
oboannotation
Access annotations of biomedical ontologies
-
jean_blosum
BLOSUM feature for jean
-
rust-ena
ena-crate interacts directly with the European Nucleotide Archive(ENA)
-
mzalign
Align peptidoforms while with mass-based alignment
-
bsalign_sys
Rust bindings for the bsalign C library
-
pdb-handler
functions to handle PDB files
-
kira-protein-pruner
High-performance protein analysis tools
-
crast
Context RNA Alignment Search Tool
-
rsomics-bam-markdup
Mark or remove PCR/optical duplicates in sorted BAM — Rust port of samtools markdup
-
redskull
A conda recipe generator for Rust crates
-
tikhonov
Harmony2 single-cell data integration (pure Rust)
-
handlegraph
in variation graphs
-
filter-clipped
A bam/sam util to filter out highly clipped NGS reads from alignment files
-
seq_io_parallel
A map-reduce style parallel extension to seq_io
-
jean
Computational biology utility library for Rust featuring sequence alignment, genome annotation, and I/O of biological files
-
nale
that performs profile Hidden Markov Model (PHMM) biological sequence alignment
-
d4utils
The CLI utils for D4 file format
-
cf1-rs
Fast construction of compacted reference de Bruijn graphs
-
exon-bed
Subcrate of the
exoncrate for working with BED files -
noodles-fastq
FASTQ format reader and writer
-
consprob-trained
Trainable Probability Inference Engine on RNA Structural Alignment
-
jellyfish-reader
Pure Rust reader for Jellyfish k-mer counting output files
-
tracksmith
A genome visualization tool written in Rust
-
filterx_engine
The engine library for filterx
-
gapsmith-transport
Transporter detection for gapsmith (port of src/transporter.sh + analyse_alignments_transport.R)
-
phantompurger-rs
Detecting chimeric molecules in scRNAseq
-
bedrs
Genomic interval library in rust
-
fqtk
A toolkit for working with FASTQ files
-
ffforf
fasta/q/x file format parser. Well fuzzed.
-
gtars-fragsplit
Small utility that wil split fragments files according to pseudobulk assignments
-
noodles-gff
Generic Feature Format (GFF) reader and writer
-
microBioRust-seqmetrics
Microbiology friendly bioinformatics Rust functions
-
census-proteomics
working with proteomics data quantified by the Census algorithm
-
prot_translate
Translate nucleotide sequence to protein
-
rustalign-io
Ultrafast DNA sequence aligner using FM-index and Smith-Waterman
-
fastxgz
A fasta/fastq parser for both compressed and not compressed files
-
fgumi-umi
UMI assignment strategies and utilities for fgumi
-
gtars-overlaprs
Genomic interval overlap operations in Rust
-
genotype_lang_py_tree
Genotype language Python target AST crate
-
rsomics-tsv-select
Select, reorder, or rename columns from TSV files — cut + awk for bioinformatics pipelines
-
use-amino-acid
Primitive amino acid vocabulary for RustUse
-
use-biological-cell
Primitive cell vocabulary for RustUse
-
exon-fastq
FASTQ support for Exon
-
cyto-io
Ultra high-throughput processing of 10x-flex single-cell sequencing data
-
rsomics-gc-windows
Compute per-window GC content across a FASTA reference — BED output for CNV/WGS normalization
-
doiTAG
doiTAG for sequence DOIs
-
papasmurf-py
PyO3 bindings and Python interface to PAPASMURF, a Platform-Accelerated Package for Alignment-free SMURF analysis
-
kira-ls-aligner
Unified short- and long-read sequence aligner written in Rust 2024. It combines minimap2-style minimizers and chaining with BWA-MEM2-style exact-match anchoring and output semantics…
-
obographs-dev
Load Obographs data files
-
microBioRust-heatmap
Microbiology friendly bioinformatics Rust functions
-
ff_kinetics
fuzzyfold's stochastic secondary structure simulations
-
fire-fasta
Ultra-fast, lazy, zero-copy Multi-FASTA parser
-
genotype_json_converter
Genotype language JSON tree converter crate
-
refget-model
Domain types for GA4GH refget Sequences and Sequence Collections APIs
-
kira-spliceqc
Deterministic, explainable splicing QC for single-cell expression data
-
fxtools
A collection of commandline Fasta/Fastq utility tools
-
noodles-htsget
An htsget client
-
flow-tru-ols
TRU-OLS (Truncated ReUnmixing OLS) algorithm for flow cytometry unmixing
-
imgt
Access the IMGT database from Rust
-
bwa-mem2-rs
Safe Rust API for bwa-mem2 alignment with caller-owned parallelism
-
kam-core
Core types and traits for alignment-free variant detection
-
genotype_lang_ts_codegen
Genotype language TypeScript target codegen crate
-
use-biological-system
Primitive biological system vocabulary for RustUse
-
seq_geom_parser
Parser and extractor for sequencing read geometry descriptions
-
genotype_lang_rs_tree
Genotype language Rust target AST crate
-
fqcat
rapidly merging FASTQ files. Never use cat again!
-
gapsmith-fill
FBA / pFBA / gap-filling via good_lp + HiGHS for gapseq
-
refget-digest
GA4GH refget digest computation: SHA-512/24 (sha512t24u) and RFC 8785 JSON Canonicalization
-
genotype_lang_ts_tree
Genotype language TypeScript target AST crate
-
seqcol_rs
implement seqcol in rust
-
exon-mzml
Exon MzML
-
kira-proteoqc
Deterministic, explainable proteostasis QC for single-cell expression data
-
nafcodec-py
PyO3 bindings and Python interface to the nafcodec crate
-
rsomics-consensus
Compute consensus sequence from a multiple sequence alignment — majority-rule or threshold
-
rustalign-common
Ultrafast DNA sequence aligner using FM-index and Smith-Waterman
-
use-reproduction
Primitive reproduction vocabulary for RustUse
-
rsomics-minimap2
Long/short-read aligner — CLI wrapper of minimap2 FFI bindings (Quadrant ②)
-
rna-algos
RNA Bioinformatics Algorithms
-
rsomics-count-matrix
Merge multiple featureCounts/htseq-count outputs into a single gene × sample count matrix
-
tca
A platform for scientific data processing and analysis
-
noodles-gtf
Gene Transfer Format (GTF) reader and writer
-
use-species
Primitive species naming vocabulary for RustUse
-
yara-mapper
Safe Rust wrapper for the YARA read mapper
-
ragc-common
Common data structures and utilities for the ragc AGC genome compression library
-
kira-spatial-3d
Deterministic 3D mesh, contour, and export primitives for spatial omics fields
-
kira-cdh
Single-binary, CLI-compatible replacement for CD-HIT utilities (cd-hit, cd-hit-est, cd-hit-2d, cd-hit-est-2d) in Rust
-
cyto-workflow
Ultra high-throughput processing of 10x-flex single-cell sequencing data
-
kira-riboqc
Deterministic ribosome and translation-state quality control for single-cell RNA-seq
-
kira-spatial-field
Gene-field extraction and deterministic signal transforms for spatial transcriptomics
-
rsomics-barcode-rank
Barcode rank statistics from a counts-per-barcode file — knee plot data for single-cell QC
-
use-life-stage
Primitive life stage vocabulary for RustUse
-
gia
set theoretic operations of genomic intervals
-
gapsmith-find
Pathway/reaction finder for gapsmith: selects pathways, orchestrates alignment, classifies hits, scores completeness
-
rsomics-nj-tree
Neighbor-joining tree construction from a distance matrix — outputs Newick
-
rsomics-bam-coverage
Per-reference coverage histogram from BAM — Rust port of samtools coverage
-
mzident
Handle all kinds of identified peptidoform files
-
fxread
A barebones fastx reader for rust
-
exon-sam
Exon SAM
-
kira-fastq
High-performance FASTQ reader with mmap-first design. Supports plain, gzip, and BGZF inputs; optional multi-line parsing; and explicit paired-end reading.
-
piscem-infer
A flexible tool to perform target quantification from bulk-sequencing data
-
guide-counter
Fast and accurate guide counting for CRISPR screens
-
primer3-tool
Command-line tool for PCR primer design and thermodynamic calculations
-
cpr
CapR, Efficient RNA Context Probability Estimator
-
rustalign-simd
Ultrafast DNA sequence aligner using FM-index and Smith-Waterman
-
rsomics-peak-count
Count BAM reads per BED peak region — ChIP-seq/ATAC-seq QC and quantification
-
prepare_fasta
Compute hash-based signatures of sequence, and perform pre-processing
-
rsomics-vcf-stats
Basic VCF variant statistics — SNP/indel counts, Ti/Tv ratio
-
rsomics-tpm
TPM and FPKM normalization of gene count matrices given gene lengths
-
ncbi-vdb-sys
FFI library for the NCBI VDB
-
rsomics-vcf-isec
VCF intersection — find shared variants between two VCFs (bcftools isec)
-
rsomics-msa-trim
Trim MSA columns by gap fraction — Rust replacement for trimAl -gt
-
rsomics-gff-grep
Filter GFF/GTF features by attribute regex — extract genes by name
-
kira-irreversibility
Deterministic irreversibility scoring for time-series state trajectories
-
gapsmith-io
I/O helpers for gapsmith: model (de)serialization (CBOR/JSON), paths, TSV/FASTA utilities
-
mzannotate
Handle fragmentation of (complex) peptidoforms
-
noodles-refget
A refget client
-
kira-mitoqc
Deterministic mitochondrial QC scoring for single-cell expression matrices
-
use-tissue
Primitive tissue vocabulary for RustUse
-
kira-scio
Deterministic single-cell input reader stack for MTX/H5AD/BD Rhapsody in Kira tools
-
sce
importing and managing various single-cell matrices
-
rsomics-popgen-core
Population-genetics primitives: π, Watterson's θ, Tajima's D, Hardy-Weinberg exact, LD r². Layer A primitive.
-
rsomics-vcf-to-bed
Convert VCF variant positions to BED intervals
-
fgumi-metrics
Structured metric types and TSV writer for fgumi operations
-
rsomics-bam-depth
Per-base or per-region depth from BAM — Rust port of samtools depth
-
mudskipper
Convert genomic alignments to transcriptomic BAM/RAD files
-
rsomics-bed-slop
Extend BED intervals by a fixed amount — bedtools slop equivalent
-
fgumi-bgzf
BGZF block reading, decompression, and compression utilities
-
cyto-cli
Ultra high-throughput processing of 10x-flex single-cell sequencing data
-
rustalign-concurrency
Ultrafast DNA sequence aligner using FM-index and Smith-Waterman
-
panscape
ensemblcov for human genomics
-
exon-gtf
GTF datasource for Exon
-
fgumi-dna
DNA sequence utilities: complement, reverse-complement, 2-bit encoding
-
kira_cdh_compat_fastq_reader
Streaming FASTQ reader compatible with CD-HIT input handling (plain and .gz), safe idiomatic Rust API; sync and async
-
af-anndata
converting alevin-fry output to the AnnData format
-
disambiseq
Create unambiguous one-off mismatch libraries for DNA sequences
-
gapsmith-medium
Rule-based medium inference — port of gapseq's predict_medium.R
-
fg-stitch
Stitch is an aligner for long reads against one or more reference/expected vector/plasmid/construct(s)
-
rsomics-pgen
PLINK1 .bed / .bim / .fam genotype-matrix reader + writer for the rsomics-* tool family. Layer A primitive.
-
kira-secretion
Deterministic, explainable secretion-state QC for single-cell expression data
-
rsomics-taxonomy
NCBI taxdump parser + LCA + lineage helpers for the rsomics-* tool family. Layer A primitive.
-
refget-rs
GA4GH refget Sequences v2.0.0 and Sequence Collections v1.0.0 in Rust
-
exon-fasta
reading and writing FASTA files with Exon
-
fgumi-sam
SAM/BAM record utilities, CIGAR parsing, and read-pair clipping for fgumi
-
phyloprob
Program, which Predicts Average Posterior Probabilities on RNA Structural Alignment
-
rsomics-bed-makewindows
Divide genome into fixed-size tiling windows — bedtools makewindows
-
rsomics-fasta-grep
Filter FASTA records by name regex — seqkit grep equivalent for FASTA
-
use-sequence-id
Primitive biological sequence identifier vocabulary for RustUse
-
rsomics-debruijn
de Bruijn graph types + linear-path collapse + unitig extraction for the rsomics-* tool family. Layer A primitive.
-
fg-sra-vdb
Safe Rust wrappers over the NCBI VDB C library
-
kira_cdh_compat_clstr
CD-HIT-compatible .clstr writer/reader and a semantic diff CLI