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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.
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bio-seq
Bit packed and well-typed biological sequences
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noodles
Bioinformatics I/O libraries
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bqtools
A command-line tool for interacting with BINSEQ file formats
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fqkit
cross-platform program for fastq file manipulation
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plascad
PlasCAD
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merkurio
Quick k-mer-based FASTA/FASTQ sequence record extraction, and SAM/BAM record filtering plus file annotation with k-mer tags
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seq_io
Fast FASTA, FASTQ and FASTX parsing
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packed-seq
Constructing and iterating packed DNA sequences using SIMD
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lt-fm-index
FM-index using k-mer lookup table for exact pattern matching
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rustyms
handle proteomic mass spectrometry data and match peptides to spectra
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matchtigs
Different algorithms for computing small and minimum plain text representations of kmer sets
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bio-forge
A pure Rust library and CLI for the automated repair, preparation, and topology construction of biological macromolecules
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bigtools
associated tools for reading and writing bigwigs and bigbeds
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simd-minimizers
A SIMD-accelerated library to compute random minimizers
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cardio-rs
computing heart rate variability (HRV) metrics from ECG and PPG data
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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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sigalign
A Similarity-Guided Alignment Algorithm
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nanocount
A dual-guide protospacer counter for long-read nanopore data
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nucs
working with nucleotide and amino acid sequences
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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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noodles-vcf
Variant Call Format (VCF) reader and writer
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mbf-fastq-processor
The fast, reliable multitool of FASTQ processing
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lightmotif-tfmpvalue
Rust reimplementation of TFMPvalue for the lightmotif crate
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bio_apis
DNA and RNA sequence types and functions
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fakit
program for fasta file manipulation
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mzdeisotope
deisotope and charge state deconvolve mass spectra
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orthanc_sdk
Orthanc plugin SDK
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dnacomb
Count the occurances of structured sequence reads and compare to an expected library
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noodles-csi
Coordinate-sorted index (CSI) format reader and writer
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gtars
Performance critical tools for genomic interval analysis
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noodles-bcf
Binary Call Format (BCF) reader and writer
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convert-af
converting alevin-fry output to the AnnData format
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noodles-tabix
Tabix (TBI) format reader and writer
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nanalogue
BAM/Mod BAM parsing and analysis tool with a single-molecule focus
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simd-sketch
A SIMD-accelerated library to compute a b-bit bottom-h sketch
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seq-hash
A SIMD-accelerated library to compute hashes of DNA sequences
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noodles-cram
CRAM format reader and writer
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pure-onnx-ocr-sync
【Sync Version】Pure Rust OCR pipeline that runs PaddleOCR DBNet + SVTR ONNX models without C/C++ dependencies
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pdbtbx
open/edit/save (crystallographic) Protein Data Bank (PDB) and mmCIF files
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faimm
Random access to indexed fasta using a mmapped file
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noodles-fasta
FASTA format reader and writer
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gtars-cli
Performance critical tools for genomic interval analysis. This is the CLI
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noodles-sam
Sequence Alignment/Map (SAM) format reader and writer
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genedex
A small and fast FM-Index implementation
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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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ffcharge
A lightweight pure Rust library for fast, residue-based force field charge assignment (AMBER/CHARMM) in molecular modeling pipelines
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noodles-bam
Binary Alignment/Map (BAM) format reader and writer
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fuzzyfold
Nucleic acid secondary structure kinetics
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dgcount
Dual guide CRISPR counter
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noodles-util
noodles support utilities
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ome_zarr_metadata
OME-Zarr (previously OME-NGFF) metadata
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mzcore
Core logic for handling massspectrometry in Rust
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noodles-bed
BED (Browser Extensible Data) reader and writer
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termal-msa
A viewer of multiple sequence alignments, with a text user interface
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noodles-gtf
Gene Transfer Format (GTF) reader and writer
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microBioRust
Microbiology friendly bioinformatics Rust functions
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mzalign
Align peptidoforms while with mass-based alignment
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rusty-dna
Normalize consumer DNA genotype exports into structured SNP data via provider-specific parsers
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noodles-fastq
FASTQ format reader and writer
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minet_ai
MiNET AI (Miniaturized Neural Evolutionary Topology) is a minimalistic Rust library that evolves small neural networks via genetic algorithm. With a focus on producing compact, adaptive…
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butter2d
Butterworth filter for image processing
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orthanc_client_ogen
Orthanc API client library produced by OpenAPI Generator
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smyl
Artificial Neuronal Network in Rust
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sais_drum
SAIS algorithm for suffix array construction
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orthanc_api
Orthanc API hand-written response models
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umgap
The Unipept Metagenomics Analysis Pipeline
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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.
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mzdeisotope-map
deisotope and charge state deconvolve mass spectra
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noodles-htsget
An htsget client
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noodles-refget
A refget client
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fastq
A parser for fastq
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mikan-rs
A medical image kit for segmentation metrics evaluation, native Rust support, and Python bindings for cross-language performance
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mzdeisotoper
Deisotoping and charge state deconvolution of mass spectrometry files
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ff_structure
fuzzyfold's secondary structure representations
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mzident
Handle all kinds of identified peptidoform files
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cigar-lodhi-rs
Lodhi subsequence kernel on CIGAR strings
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seqtk-rs
sequence processing tool written in Rust for manipulating FASTA/FASTQ files. Pure rust version of seqtk.
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xdf
Read XDF Files
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abpoa-rs
Rust bindings for abPOA: Adaptive Banded POA
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finalspark-rs
live data recording from MEA devices
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mzannotate
Handle fragmentation of (complex) peptidoforms
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mzcv
Handle controlled vocanulaires (CVs) and ontologies, both statically and dynamically
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ff_energy
fuzzyfold's nearest neighbor free energy evaluations
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imgt
Access the IMGT database from Rust
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ff_kinetics
fuzzyfold's stochastic secondary structure simulations
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votesmart
A client wrapper for the Votesmart REST API
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genomers
Package to download NCBI genome data and metadata
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faloops
Counter-attack nonhuman bad actors that abuse Frequency-shift Keying and Phase-shift Keying in your human environment thusly soothing your temporal and occipital lobes
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af-anndata
converting alevin-fry output to the AnnData format
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burn_dragon_hatchling
burn (baby) dragon hatchling inference and training
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strobemers-rs
strobemers
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rustynuc
Quick analysis of pileups for likely 8-oxoG locations
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noodles-core
Shared utilities when working with noodles
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mni2mz3
Brain imaging surface mesh file format converter
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bamsalvage
Rust version of bamsalvage, retrieving sequences from a corrupted BAM file as much as possible
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psylink
GUI for PsyLink neural interface for receiving/graphing biosignals and predicting user's intentions
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microBioRust-seqmetrics
Microbiology friendly bioinformatics Rust functions
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fastats
CLI to generate FASTA file statistics (masking, GC content, etc.)
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fire-fasta
Ultra-fast, lazy, zero-copy Multi-FASTA parser
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nii-rs
reading/writing NIfTI files, with SimpleITK/Nibabel-like APIs, native Rust support, and Python bindings for cross-language performance
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nwbview
Neurodata Without Borders viewer
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ggetrs-ncbi
ggetrs submodule for querying NCBI
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bvreader
Reader for the BrainVision data format
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ggetrs-pdb
ggetrs submodule for querying PDB
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ggetrs-ucsc
ggetrs submodule for querying UCSC
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ggetrs-info
ggetrs submodule for querying information about genes
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ggetrs-enrichr
ggetrs submodule for querying ENRICHR
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sdust
symmetric DUST algorithm, with optional CLI
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ggetrs-seq
ggetrs submodule for querying sequence information
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burn_hatchling
burn (baby) dragon hatchling inference and training
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burn_bdh
burn baby dragon hatchling inference and training
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mmr
Minimap2 CLI written in rust using bindings with BINSEQ and VBINSEQ support
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mzsvg
draw mass spectra
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ggetrs-ensembl
ggetrs submodule for querying ENSEMBL
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digest-rs
Rust bindings for the digest library
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ggetrs-uniprot
ggetrs submodule for querying UNIPROT
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encryptodon
Pachyderm Goes Private 🐘🕶️
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rust-gc-count
GC and sequence utilities
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elm
A minimalist framework for Extreme Learning Machines (ELMs)
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ggetrs-archs4
ggetrs submodule for querying archs4
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ggetrs-chembl
ggetrs submodule for querying CHEMBL
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aa2nucaln
Convert an amino acid alignment into a nucleotide alignment
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ggetrs-blast
ggetrs submodule for querying BLAST
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GetPDB
Download Protein files from rcsb.org
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ncrs
A lightweight Rust library for loading and storing nucleic acid sequences (DNA or RNA) and their annotations with minimum dependences
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abpoa-sys
Automatically generated FFI definitions for abPOA
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gffkit
program for gff3 file manipulation
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