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minimap2
Bindings to libminimap2
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perbase
Fast and correct perbase BAM/CRAM analysis
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bio-seq
Bit packed and well-typed biological sequences
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atg
Convert transcripts between different file formats
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ragc-cli
Command-line interface for the ragc AGC genome compression tool
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eVaiutilities
variant analyzer for human genomics
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google-genomics1-cli
A complete library to interact with genomics (protocol v1)
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rustybam
bioinformatics toolkit in rust
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generic_a_star
A generic implementation of the A* algorithm
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google-genomics1
A complete library to interact with genomics (protocol v1)
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lightmotif
A lightweight platform-accelerated library for biological motif scanning using position weight matrices
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verify-same-kmer-content
Verify that an SPSS has the same kmer content as a set of unitigs
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predictosaurus
Uncertainty aware haplotype based genomic variant effect prediction
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bed-reader
Read and write the PLINK BED format, simply and efficiently
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orphos-cli
Command-line interface for Orphos, a tool for finding protein-coding genes in microbial genomes
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rust-bio-tools
A set of fast and robust command line utilities for bioinformatics tasks based on Rust-Bio
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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.
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ibu
high throughput binary encoding genomic sequences
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biometal
ARM-native bioinformatics library with streaming architecture and evidence-based optimization
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efficient_pca
Principal component computation using SVD and covariance matrix trick
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toxannotator
tox annotator for ToxDB
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superintervals
Interval overlap library
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varlociraptor
calling of genomic variants using a latent variable model
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kmerutils
Kmer counting, hashing, sequence sketching
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seed_chain
A seeding and generic chaining mechanism for sequence-to-sequence alignment
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lib_tsshow
A visualiser for template-switch alignments
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varlinker
human genomics
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seqkmer
High-performance FASTA/FASTQ IO and minimizer-based k-mer analysis utilities for Rust bioinformatics pipelines
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phyloEvolve
variant analyzer for human genomics
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vcfilter
human genomics
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oxbow
Read conventional genomic file formats as data frames and more via Apache Arrow
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gffx
An ultra-fast and memory-efficient toolkit for querying GFF files, written with Rust
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xsra
A performant and storage-efficient CLI tool to extract sequences from an SRA archive with support for FASTA, FASTQ, and BINSEQ outputs
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fasterp
High-performance FASTQ preprocessing tool - often faster than fastp with the same interface
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d4
file format implementation
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deacon
Fast DNA search and [host] depletion using minimizers
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rust-featurecounts
A fast feature counting tool for prokaryotic RNA-seq analysis, compatible with featureCounts
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tidk
A toolkit for finding telomeric repeats in a genome
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tsalign
A sequence-to-sequence aligner that accounts for template switches
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ensemblcov
human genomics
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seqwish
A variation graph inducer - build pangenome graphs from pairwise alignments
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sweepga
Efficient pangenome alignment filtering and sparsification tool
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segul
An ultrafast and memory-efficient tool for phylogenomics
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CAGrepeat-analyzer
CAG repeat for human genomics
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atglib
handle transcripts for genomics and transcriptomics
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d4-framefile
The Framefile container crate for D4 file format
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slow5
interacting with slow5
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orphos-core
Core library for Orphos, a tool for finding protein-coding genes in microbial genomes
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mehari
Variant effect prediction all in Rust
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gtars
Performance critical tools for genomic interval analysis
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coitrees
A very fast data structure for overlap queries on sets of intervals
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convert-af
converting alevin-fry output to the AnnData format
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ska
Split k-mer analysis
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noodles-tabix
Tabix (TBI) format reader and writer
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iitree-rs
Implicit augmented interval tree (IAITree/cgranges) with memory-mapped disk storage
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fqtk
A toolkit for working with FASTQ files
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lib_tsalign
A sequence-to-sequence aligner that accounts for template switches
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feagi_data_structures
The most core library, defines the basic data types used by FEAGI, as well as some processors to modify them
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sketchlib
Genome and amino-acid sketching
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bamslice
Extract byte ranges from BAM files and convert to interleaved FASTQ format for parallel processing
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bigsig
Large-scale Sequence Search with BItsliced Genomic Signature Index (BIGSIG)
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gtars-cli
Performance critical tools for genomic interval analysis. This is the CLI
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htsgetr
htsget protocol server implementation in Rust
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markov_genome
Learn the properties of a FASTA sequence database and simulate sequences in a Markov process
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fqgrep
Search a pair of fastq files for reads that match a given ref or alt sequence
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binseq
A high efficiency binary format for sequencing data
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kbo
Local alignment search with k-bounded matching statistics
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onecode
Rust bindings for ONEcode - a data representation format for genomic data
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bsxplorer2
A high-performance library for bisulfite sequencing data analysis and DNA methylation research
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infer_sex
A high-performance, zero-dependency Rust library for inferring sex from variant data
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gia
set theoretic operations of genomic intervals
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d4-hts
The htslib binding used by D4
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noodles-gff
Generic Feature Format (GFF) reader and writer
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d4-bigwig
The libBigWig binding used by D4
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kbo-cli
Command-line interface to the kbo local aligner
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microBioRust
Microbiology friendly bioinformatics Rust functions
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gtars-genomicdist
Rust port of GenomicDistributions: tools for computing statistics for genomic interval sets
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seqcol_rs
implement seqcol in rust
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genomicsqlite
Genomics Extension for SQLite
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covar
Calls physically-linked mutation clusters from wastewater amplicon sequencing data
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bacdive
analyzer for microbial genomics
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diced
reimplementation of the MinCED algorithm for identifying CRISPRs in full or assembled genomes
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ebiotic
interacting with common bioinformatics web services
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ragc-core
Core compression and decompression algorithms for the AGC genome compression format
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gtars-igd
IGD: a high-performance genomic interval search tool
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d4tools
The CLI utils for D4 file format
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gtars-io
Small, io focused crate for gtars
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bed-utils
manipulating genomic range objects
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rustynetics
A high-performance genomics libary specialized in handling BAM and BigWig files
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panscape
ensemblcov for human genomics
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blobtk
Core utilities for BlobToolKit
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fmlrc
FM-index Long Read Corrector - Rust implementation
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scattr
estimating the copy number of large tandem repeats
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d4utils
The CLI utils for D4 file format
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msbwt2
multi-string BWT query library
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guide-counter
Fast and accurate guide counting for CRISPR screens
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grass-runtime
Runtime library for GRASS
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libprosic
calling of genomic variants using a latent variable model
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gtars-overlaprs
Genomic interval overlap operations in Rust
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cribtools
CLI for reading genome track files
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omics
Foundations for omics analysis using Rust
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gtars-fragsplit
Small utility that wil split fragments files according to pseudobulk assignments
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bsxplorer-ci
A high-performance tool for bisulfite sequencing data analysis and DNA methylation research
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granges
command line tool for genomic range operations
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microBioRust-heatmap
Microbiology friendly bioinformatics Rust functions
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chainfile
working with genomics chain files
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grangers
working with genomic ranges and annotations
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seqpls
My sequences please - a paired fastq grepper with regex support
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ragc-common
Common data structures and utilities for the ragc AGC genome compression library
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gtars-uniwig
uniwig: a tool for computing coverage from BED files over genomic intervals
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grass-ir
IR for GRASS
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gtars-scoring
Small, rust utility to compute read overlaps of fragments files over a universe
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gtars-refget
refget standard for accessing reference sequences
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gtars-bbcache
bbcache: a caching system for BED files on bedbase.org
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bio-streams
Streaming bioinformatics data types
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google-genomics1_beta2
A complete library to interact with genomics (protocol v1beta2)
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bigbed
dealing with BigBed files
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rumi
PCR Deduplication via directional adjacency
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mudskipper
Convert genomic alignments to transcriptomic BAM/RAD files
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nthash
rolling hash function for hashing all possible k-mers in a DNA sequence
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readfish-tools
Tools for analysing adaptive sampling data
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ffforf
fasta/q/x file format parser. Well fuzzed.
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genomap
A small library for storing generic genomic data indexed by a chromosome
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gen
A sequence graph and version control system
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tf-binding-rs
Fast transcription factor binding site prediction and FASTA manipulation in Rust
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pipspeak
converting PIPSeq files to 10X Genomics compatible FASTQ files
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roers
prepare augmented annotations for single-cell RNA-seq analysis
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bird_tool_utils
Microbial genomics utility functions
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recmap
reading and working with recombination maps in Rust
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gtars-tokenizers
Genomic region tokenizers for machine learning in Rust
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af-anndata
converting alevin-fry output to the AnnData format
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goat-cli
Query metadata for any species across the tree of life
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hyper-gen
HyperGen is a high-performance Rust library to sketch genomics files into hypervectors and realize fast Average Nucleotide Identity (ANI) approximation
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bindash
One Permutation Hashing, Optimal Densification, Genomics
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rsrs
command line tool to compute seqcol objects and digests
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ncbi-vdb-sys
FFI library for the NCBI VDB
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myte
phylogenomic tree building
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fasta_windows
Make quick statistics in windows from a fasta file
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microbiorust-py
Microbiology friendly bioinformatics Rust functions
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read-structure
parsing and working with read structure descriptions
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microBioRust-seqmetrics
Microbiology friendly bioinformatics Rust functions
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diced-py
PyO3 bindings and Python interface to the diced crate
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bitnuc-mismatch
Create unambiguous one-off mismatch hash tables from bitnuc scalars
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genomic_interval_pipeline
A pipeline for creating HDF5 databases from genomic intervals
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grass-macro
Procedual Macros for GRASS
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omics-variation
Foundational representations of variation in the Rust omics ecosystem
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fg-stitch-lib
Stitch aligner implementation and supporting utilities
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gtars-core
Core library for gtars: tools for high performance genomic interval analysis
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gannot
A small library with limited functionality focused on genome annotation
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ambigviz
Identify and plot ambiguous nucleotide bases at given positions from a BAM file
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nucleobases
low-level brick crate for managing nucleobases as data in code
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gtokenizers
tokenizing genomic data with an emphasis on region set data
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omics-molecule
Foundational representations of biological molecules in the Rust omics ecosystem
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gkl
Genomics Kernel Library
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vcf_add_ids
Add IDs to VCF records
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rsvart
A small library for representing genomic variants and regions
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slow5lib-sys
Low-level bindings to the slow5lib C library
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gtfjson
convert GTF files to newline-delim JSON
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genezip
An encoding CLI tool for compressing and decompressing raw genome information
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digest-rs
Rust bindings for the digest library
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genimtools
Performance-critical tools to manipulate, analyze, and process genomic interval data. Primarily focused on building tools for geniml - our genomic machine learning python package.
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spdi
format to describe a genomic variant. This crate provides a library to get an SPDI format representation of a variant and a command-line utility which adds SPDI format output to an input VCF file.
-
simplr
An augmented execution context to simplify long-read transcriptome analysis
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ehxacto
Find exact tandem repeat coordinates from approximate regions identified by ExpansionHunter denovo
-
ullar
A high-performance, accessible phylogenomic pipeline
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genomic
A small crate for implementing genetical algorithms
-
scispeak
converting Sci-RNA-Seq3 files to 10X Genomics compatible FASTQ files
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aa2nucaln
Convert an amino acid alignment into a nucleotide alignment
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bgzf
working with explicitly BGZF compressed data
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rustbam
Rust-powered BAM depth extraction with Python bindings
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cgt_bacpop
Label core and rare genes in pangenome dataa
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splici
generate spliced and unspliced reference transcripts for sequence alignment
-
vbinseq
A high efficiency binary format for sequencing data with variable-length records
-
bedblocks
Split a BED file into blocks
-
gene-extractor
Extract multiple genes in genomic contigs using reference fasta file
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