-
needletail
FASTX parsing and k-mer methods
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rust-lapper
A fast and easy interval overlap library
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rust-htslib
HTSlib bindings and a high level Rust API for reading and writing BAM files
-
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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noodles
Bioinformatics I/O libraries
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noodles-csi
Coordinate-sorted index (CSI) format reader and writer
-
minimap2
Bindings to libminimap2
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blutils-cli
The CLI port of the blutils library
-
rasusa
Randomly subsample reads or alignments
-
bitnuc
efficient nucleotide sequence manipulation using 2-bit and 4-bit encodings
-
bqtools
A command-line tool for interacting with BINSEQ file formats
-
crankshaft
A headless task execution engine that supports local, cloud, and HPC
-
bio-seq
Bit packed and well-typed biological sequences
-
lrge
Genome size estimation from long read overlaps
-
rustqc
Fast RNA-seq QC in a single pass: dupRadar, featureCounts, 8 RSeQC tools, preseq, samtools stats, and Qualimap — reimplemented in Rust
-
vareffect-cli
CLI for vareffect — annotate genomic variants without Ensembl VEP
-
lightmotif
A lightweight platform-accelerated library for biological motif scanning using position weight matrices
-
simd-minimizers
A SIMD-accelerated library to compute random minimizers
-
sassy
Approximate string matching using SIMD
-
finch
min-wise independent permutation locality sensitive hashing ('MinHashing') for genomic data and command-line utility for manipulation
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grepq
quickly filter fastq files
-
sprocket
A command line tool for working with Workflow Description Language (WDL) documents
-
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
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packed-seq
Constructing and iterating packed DNA sequences using SIMD
-
atg
Convert transcripts between different file formats
-
htsget-config
Used to configure htsget-rs by using a config file or reading environment variables
-
perbase
Fast and correct perbase BAM/CRAM analysis
-
lowess
(Locally Weighted Scatterplot Smoothing)
-
fastLowess
High-performance LOWESS (Locally Weighted Scatterplot Smoothing)
-
crispr_screen
A fast and configurable differential expression analysis tool for CRISPR screens
-
vareffect
Variant consequence prediction and HGVS notation, concordant with Ensembl VEP
-
taxonomy
Routines for loading, saving, and manipulating taxonomic trees
-
oxo-call
Model-intelligent orchestration for CLI bioinformatics — call any tool with LLM intelligence
-
bed-reader
Read and write the PLINK BED format, simply and efficiently
-
ragc-cli
Command-line interface for the ragc AGC genome compression tool
-
fgumi-raw-bam
Raw byte-level operations on BAM alignment records
-
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
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flow-fcs
High-level Flow Cytometry Standard (FCS) file struct and operations
-
ibu
high throughput binary encoding genomic sequences
-
peacoqc-cli
Command-line tool for PeacoQC flow cytometry quality control
-
kira-spatial
Deterministic orchestrator for spatial transcriptomics: IO, field transforms, core math, and 3D export
-
hmmer-pure-rs
Pure Rust port of HMMER 3.4 — biological sequence analysis using profile HMMs
-
orphos-cli
Command-line interface for Orphos, a tool for finding protein-coding genes in microbial genomes
-
primer3-tool
Command-line tool for PCR primer design and thermodynamic calculations
-
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.
-
ldsc
LD Score Regression — fast Rust reimplementation of Bulik-Sullivan et al. LDSC
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kuva
Scientific plotting library in Rust with various backends
-
loess-rs
LOESS (Locally Estimated Scatterplot Smoothing) implementation in Rust
-
rebgzf
Efficient gzip to BGZF transcoder using Puffin-style half-decompression
-
primerpincer
A CLI primer trimming tool for long-read sequencing data
-
motif-bridge
Cross-language toolkit for converting motifs between MEME and HOMER formats
-
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…
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trim-galore
Fast adapter and quality trimming for NGS data — Oxidized Edition
-
kractor
Extract reads from a FASTQ file based on taxonomic classification via Kraken2
-
oxo-flow-cli
CLI for the oxo-flow bioinformatics pipeline engine
-
piscem
Fast, space-efficient k-mer-based read mapper for bulk RNA-seq, scRNA-seq, and scATAC-seq
-
fastx
reads Fasta and FastQ files with little overhead
-
fgumi
High-performance tools for UMI-tagged sequencing data: extraction, grouping, and consensus calling
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fgumi-consensus
Consensus calling algorithms for fgumi: simplex, duplex, and CODEC
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jam-rs
Just another (genomic) minhash (Jam) implementation in Rust
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vcfkit-cli
Fast VCF toolkit: normalize, liftover, filter — single static binary, no htslib
-
htsget-storage
Storage interfaces and abstractions for htsget-rs
-
fastdedup
A fast and memory-efficient FASTX PCR deduplication tool
-
simdna
High-performance SIMD-accelerated DNA sequence encoding supporting all IUPAC nucleotide codes
-
noodles-vcf
Variant Call Format (VCF) reader and writer
-
voronota-ltr
Voronota-LT is an alternative version of Voronota for constructing tessellation-derived atomic contact areas and volumes
-
light_phylogeny
Methods and functions for phylogeny
-
helicase
SIMD-accelerated library for FASTA/FASTQ parsing and bitpacking
-
nohuman
Remove human reads from a sequencing run
-
ontolius
A fast and safe crate for working with biomedical ontologies
-
intspan
Command line tools for IntSpan related bioinformatics operations
-
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
-
modtector
A high-performance modification detection tool in Rust
-
seqsizzle
A pager for viewing FASTQ and FASTA files with fuzzy matching, allowing different adaptors to be colored differently
-
kira-organelle
Deterministic aggregation and orchestration for the Kira organelle QC stack
-
omicsx
SIMD-accelerated sequence alignment and bioinformatics analysis for petabyte-scale genomic data
-
hashfasta
Very quickly compute hashes for FASTA/FASTQ files considering only the sequence content
-
grit-genomics
GRIT: Genomic Range Interval Toolkit - high-performance genomic interval operations
-
umi-tools-rs
A fast drop-in replacement for UMI-tools, written in Rust
-
diced
reimplementation of the MinCED algorithm for identifying CRISPRs in full or assembled genomes
-
kam-pathfind
De Bruijn graph construction and variant path walking
-
compact-genome
Representation of genomes
-
gapsmith-cli
Command-line interface for gapsmith
-
mim-index
Small index enabling multithreaded fastq.gz decompression
-
kam-call
Statistical variant calling with confidence intervals
-
barbell
Extremely fast and accurate Nanopore demultiplexing
-
fasten
A set of scripts to run basic analysis on fastq files
-
biometal
ARM-native bioinformatics library with streaming architecture and evidence-based optimization
-
seqkmer
High-performance FASTA/FASTQ IO and minimizer-based k-mer analysis utilities for Rust bioinformatics pipelines
-
genomicframe-core
High-performance genomics I/O and interoperability layer
-
sigalign
A Similarity-Guided Alignment Algorithm
-
minimap2-temp
Bindings to libminimap2
-
kam-index
K-mer indexing with molecule-level evidence tracking
-
sequenceprofiler
sequence similarity based on identity kmers and all sequence profiling under one rust crate
-
cgkitten
Convert mmCIF/PDB protein structures to coarse-grained representation with Monte Carlo titration
-
bio-forge
A pure Rust library and CLI for the automated repair, preparation, and topology construction of biological macromolecules
-
kira-microenvironment
Deterministic, explainable ligand-receptor microenvironment interaction scoring for single-cell expression data
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htsget-http
handling HTTP in htsget-rs
-
peacoqc-rs
PeacoQC quality control algorithms for flow cytometry
-
primer3
Safe Rust bindings to the primer3 primer design library
-
orphos-core
Core library for Orphos, a tool for finding protein-coding genes in microbial genomes
-
multiseqex
Multi-sequence extractor from FASTA using FAI indexing, with parallelism and flexible region input formats
-
oxbow
Read conventional genomic file formats as data frames and more via Apache Arrow
-
fgumi-bgzf
BGZF block reading, decompression, and compression utilities
-
kam-bio
Alignment-free variant detection for duplex UMI sequencing
-
kira-qc
FastQC-compatible QC tool written in Rust
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ferro-hgvs
HGVS variant normalizer - part of the ferro bioinformatics toolkit
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nwr
**N**CBI taxonomy and assembly **WR**angler
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microBioRust
Microbiology friendly bioinformatics Rust functions
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hgvs-weaver
High-performance HGVS variant mapping and validation engine
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mi2graph
Generate MIC relations between features with dynamic feature filtering for graph initialization
-
flow-plots
Package for drawing and interacting with plots in flow cytometry data
-
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
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gapsmith-db
Loaders for gapseq's reference data tables (SEED, MNXref, biomass JSON, pathway tables)
-
gapsmith-core
Core types for gapsmith: Model, Reaction, Metabolite, StoichMatrix, GPR
-
rust-bio-tools
A set of fast and robust command line utilities for bioinformatics tasks based on Rust-Bio
-
varforge
Synthetic cancer sequencing test data generator
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gdock
Information-driven protein-protein docking using a genetic algorithm
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scdata
High-performance Rust library for constructing sparse single-cell UMI count data with deterministic MatrixMarket export
-
oxo-flow-venus
Venus: clinical-grade tumor variant detection pipeline built on oxo-flow
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prodigal-rs
Prokaryotic gene prediction — Prodigal rewritten in Rust
-
parasail-rs
Rust bindings and wrapper for parasail, a SIMD C library for pairwise sequence alignment
-
kira-nuclearqc
Deterministic CLI for nuclear state and transcriptional plasticity analysis from 10x scRNA-seq MTX inputs
-
atria-rs
running the Ablatio Triadum (ATria) centrality algorithm (Cickovski et al, 2015, 2017)
-
rapidtrees
Fast pairwise tree distance calculations (Robinson-Foulds, Weighted RF, Kuhner-Felsenstein) for phylogenetic trees
-
fg-sra
High-performance SRA-to-SAM/BAM converter replacing NCBI sam-dump
-
librna-sys
Low-level bindings for the ViennaRNA library
-
sgcount
A fast and flexible sgRNA counter
-
pdbrust
A comprehensive Rust library for parsing and analyzing Protein Data Bank (PDB) files
-
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.
-
quadrank
Fast rank over binary and size-4 DNA alphabets
-
noodles-tabix
Tabix (TBI) format reader and writer
-
ensemblcov
human genomics
-
genomic-system-finder-cli
Command-line interface for detecting macromolecular systems in microbial genomes
-
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
-
redicat
RNA Editing Cellular Assessment Toolkit: A highly parallelized utility for analyzing RNA editing events in single-cell RNA-seq data
-
fasterp
High-performance FASTQ preprocessing tool - often faster than fastp with the same interface
-
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
-
ref-solver
Solve reference genome identification from BAM/SAM headers
-
stela-int-to-str
Fast integer to string conversion utilities optimized for high-throughput data processing
-
gapsmith-align
Alignment abstraction for gapsmith: blast/diamond/mmseqs2 runners + precomputed TSV ingestion
-
ugv
Ultra-fast genome viewer for interactive exploration of genomic data
-
phylo
An extensible Phylogenetics library written in rust
-
fqgrep
Search a pair of fastq files for reads that match a given ref or alt sequence
-
xloci
get sequences from 2bit/fa using bed/gtf/gff
-
gapsmith-draft
Draft model construction for gapsmith (port of src/generate_GSdraft.R + helpers)
-
blast-rs
Pure-Rust implementation of NCBI BLAST (Basic Local Alignment Search Tool)
-
bio_utils_rs
bioinformatic analysis
-
hashrope-bio
Computational biology applications of hashrope — drug resistance panels, gene-level change detection, genomic region queries, tandem repeat analysis
-
vcfkit-core
Core library for vcfkit: VCF normalize, liftover, and filter operations
-
noodles-sam
Sequence Alignment/Map (SAM) format reader and writer
-
tinyhgvs
Lightweight Rust library for parsing HGVS variants
-
rustynetics
A high-performance genomics libary specialized in handling BAM and BigWig files
-
kmerust
A fast, parallel k-mer counter for DNA sequences in FASTA and FASTQ files
-
sequintools
A suite of tools for manipulating and reporting on NGS data that has sequins added to the sample
-
kira-protein-pruner
High-performance protein analysis tools
-
fxtools
A collection of commandline Fasta/Fastq utility tools
-
haddock-restraints
Generate restraints to be used in HADDOCK
-
sourmash
tools for comparing biological sequences with k-mer sketches
-
flow-gates
Package for drawing and interacting with gates in flow cytometry data
-
rype
High-performance genomic sequence classification using minimizer-based k-mer sketching in RY space
-
sview-fmindex
FM-index library with slice view architecture for efficient text indexing and pattern matching
-
dnacomb
Count the occurances of structured sequence reads and compare to an expected library
-
genemancer
Rust CLI toolkit for niche optimized genomics file processing and target-based variant workflows
-
wham
weighted histogram analysis method
-
ksw2rs
Native Rust port of ksw2 (ksw2_extz2_sse) with stable-Rust SIMD backends
-
deacon
Accelerated DNA sequence search and [host] depletion using minimizers
-
gapsmith-transport
Transporter detection for gapsmith (port of src/transporter.sh + analyse_alignments_transport.R)
-
libsais
Bindings to the C library libsais for suffix array construction
-
ontology-registry
that lets you download, store and register ontologies
-
bgzf
working with explicitly BGZF compressed data
-
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…
-
kira-mmcif
Low-level, streaming mmCIF parser focused on protein coordinates
-
ska
Split k-mer analysis
-
bamnado
Tools and utilities for manipulation of BAM files for unusual use cases. e.g. single cell, MCC
-
hamming-resonate
Fast nearest-neighbour search over fixed-length DNA sequences using Hamming distance
-
biotools
bioinformatics CLI tools for sequence analysis and manipulation
-
flow-gate
Facade crate for flow-gate with compliance runner and benchmark binaries
-
kam-assemble
Molecule assembly from duplex UMI sequencing reads
-
doiTAG
doiTAG for sequence DOIs
-
fastLoess
High-level, parallel LOESS (Locally Estimated Scatterplot Smoothing) implementation in Rust
-
single_rust
Single-cell analysis in Rust
-
noodles-bcf
Binary Call Format (BCF) reader and writer
-
kira-autolys
Deterministic, explainable autophagy/lysosome dependency QC for single-cell expression data
-
pileup-hi
High-throughput, extensible SAM/BAM pileup generator
-
cyanea-chem
Chemistry and small molecules for the Cyanea bioinformatics ecosystem
-
odgi-ffi
A safe, ergonomic Rust wrapper for the odgi pangenome graph tool
-
cealign
Combinatorial Extension (cealign) algorithm to align protein structures
-
fastq-fix-i5
Rewrite FASTQ headers by reverse-complementing only the i5 (P5/index2) part in ...:i7+i5
-
salti
A modern, fast, multiple sequence alignment browser - built for the terminal
-
genomic-system-finder-hmm
Pure Rust HMMER3-compatible profile HMM search engine for protein sequences
-
rtemis-a3
A3 (Amino Acid Annotation) format — parse, validate, and inspect A3 JSON files
-
kira-shared-sc-cache
Shared deterministic binary cache reader/writer for Kira single-cell pipelines (kira-organelle.bin and expr.bin)
-
rvdna
— AI-native genomic analysis. 20-SNP biomarker risk scoring, streaming anomaly detection, 64-dim profile vectors, 23andMe genotyping, CYP2D6/CYP2C19 pharmacogenomics, variant calling…
-
securiety
parsing and validating CURIE IDs
-
rust_deseq2
A pure Rust implementation of DESeq2 for differential expression analysis of RNA-seq data
-
seq-hash
A SIMD-accelerated library to compute hashes of DNA sequences
-
fastars
Ultra-fast QC and trimming for short and long reads
-
fasta_rs
Multi purpose fasta toolkit
-
seqwish
A variation graph inducer - build pangenome graphs from pairwise alignments
-
cyanea-align
Sequence alignment algorithms for the Cyanea bioinformatics ecosystem
-
mbf-fastq-processor
The fast, reliable multitool of FASTQ processing
-
cyanea-phylo
Phylogenetics and trees for the Cyanea bioinformatics ecosystem
-
ARGenus
ARG detection and genus-level classification using flanking sequence analysis
-
refman
A command-line manager for bespoke reference datasets used in bioinformatic analyses
-
xpclrs
A high-performance rust implementation of the XP-CLR method
-
kira-energetics
Deterministic, explainable energy-landscape analysis for cellular states
-
deepbiop
Deep Learning Processing Library for Biological Data
-
papasmurf
Platform-Accelerated Package for Alignment-free SMURF analysis
-
rustkmer
High-performance k-mer counting tool in Rust
-
data-protocol-validator
Rust validator for Data Protocol schemas - validates versioned bioinformatics analysis output against JSON Schema-based protocol definitions
-
gapsmith-io
I/O helpers for gapsmith: model (de)serialization (CBOR/JSON), paths, TSV/FASTA utilities
-
biovault
A bioinformatics data vault CLI tool
-
cyanea-omics
Omics data structures for the Cyanea bioinformatics ecosystem
-
tsg
Deep Learning Processing Library for Biological Data
-
rnadraw
RNA secondary structure SVG renderer CLI
-
noodles-cram
CRAM format reader and writer
-
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.
-
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.
-
tru-ols
Command-line tool for TRU-OLS flow cytometry unmixing
-
genepred
port for the GenePred format in Rust
-
cyanea-ml
ML primitives for bio (embeddings, etc.) for the Cyanea bioinformatics ecosystem
-
cyanea-stats
Statistical methods for the Cyanea bioinformatics ecosystem
-
infer_sex
A high-performance, zero-dependency Rust library for inferring sex from variant data
-
nafcodec
Rust coder/decoder for Nucleotide Archive Format (NAF) files
-
raxtax
k-mer-based non-Bayesian Taxonomic Classifier
-
atglib
handle transcripts for genomics and transcriptomics
-
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
-
kam-core
Core types and traits for alignment-free variant detection
-
gapsmith-medium
Rule-based medium inference — port of gapseq's predict_medium.R
-
thaf
Extracts transcript sequences and gene maps from genome FASTA files using GFF3 annotations
-
mapping_info
Compact mapping/run metrics container and reporting utilities for sequencing read mapping pipelines
-
lightmotif-py
PyO3 bindings and Python interface to the lightmotif crate
-
kira-spatial-field
Gene-field extraction and deterministic signal transforms for spatial transcriptomics
-
seq_io_parallel
A map-reduce style parallel extension to seq_io
-
genedex
A small and fast FM-Index implementation
-
sweepga
Efficient pangenome alignment filtering and sparsification tool
-
refget-server
Axum-based GA4GH refget Sequences v2.0.0 and Sequence Collections v1.0.0 server
-
genome-sh
The jq of genomics. Fast, local, human-readable variant analysis.
-
Stellerator
Extract candidate fusion-supporting reads for target genes from indexed BAM files
-
pa-types
Core library types for global pairwise alignment
-
redskull
A conda recipe generator for Rust crates
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