-
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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blutils-cli
The CLI port of the blutils library
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minimap2
Bindings to libminimap2
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bio-seq
Bit packed and well-typed biological sequences
-
rasusa
Randomly subsample reads or alignments
-
bitnuc
efficient nucleotide sequence manipulation using 2-bit and 4-bit encodings
-
htsget-config
Used to configure htsget-rs by using a config file or reading environment variables
-
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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lrge
Genome size estimation from long read overlaps
-
perbase
Fast and correct perbase BAM/CRAM analysis
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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.
-
finch
min-wise independent permutation locality sensitive hashing ('MinHashing') for genomic data and command-line utility for manipulation
-
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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lowess
(Locally Weighted Scatterplot Smoothing)
-
atg
Convert transcripts between different file formats
-
crispr_screen
A fast and configurable differential expression analysis tool for CRISPR screens
-
kira-qc
FastQC-compatible QC tool written in Rust
-
bed-reader
Read and write the PLINK BED format, simply and efficiently
-
ragc-cli
Command-line interface for the ragc AGC genome compression tool
-
grepq
quickly filter fastq files
-
sprocket
A command line tool for working with Workflow Description Language (WDL) documents
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taxonomy
Routines for loading, saving, and manipulating taxonomic trees
-
hashfasta
Very quickly compute hashes for FASTA/FASTQ files considering only the sequence content
-
peacoqc-cli
Command-line tool for PeacoQC flow cytometry quality control
-
bqtools
A command-line tool for interacting with BINSEQ file formats
-
packed-seq
Constructing and iterating packed DNA sequences using SIMD
-
primerpincer
A CLI primer trimming tool for long-read sequencing data
-
jam-rs
Just another (genomic) minhash (Jam) implementation in Rust
-
simd-minimizers
A SIMD-accelerated library to compute random minimizers
-
ibu
high throughput binary encoding genomic sequences
-
kira-nuclearqc
Deterministic CLI for nuclear state and transcriptional plasticity analysis from 10x scRNA-seq MTX inputs
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lightmotif
A lightweight platform-accelerated library for biological motif scanning using position weight matrices
-
fastLowess
High-performance LOWESS (Locally Weighted Scatterplot Smoothing)
-
nwr
nwris a command line tool for newick and taxonomy -
loess-rs
LOESS (Locally Estimated Scatterplot Smoothing) implementation in Rust
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kractor
Extract reads from a FASTQ file based on taxonomic classification via Kraken2
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sequintools
A suite of tools for manipulating and reporting on NGS data that has sequins added to the sample
-
sassy
Approximate string matching using SIMD
-
htsget-storage
Storage interfaces and abstractions for htsget-rs
-
fastx
reads Fasta and FastQ files with little overhead
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crankshaft
A headless task execution engine that supports local, cloud, and HPC
-
quadrank
Fast rank over binary and size-4 DNA alphabets
-
flow-fcs
High-level Flow Cytometry Standard (FCS) file struct and operations
-
rumina
High-throughput UMI-aware deduplication of next-generation sequencing data
-
simdna
High-performance SIMD-accelerated DNA sequence encoding supporting all IUPAC nucleotide codes
-
light_phylogeny
Methods and functions for phylogeny
-
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
-
ontolius
A fast and safe crate for working with biomedical ontologies
-
minimap2-temp
Bindings to libminimap2
-
kun_peng
Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all
-
wdl-ast
An abstract syntax tree for Workflow Description Language (WDL) documents
-
fasten
A set of scripts to run basic analysis on fastq files
-
biometal
ARM-native bioinformatics library with streaming architecture and evidence-based optimization
-
seqtkrs
reimplementation of seqtk, a fast and lightweight tool for processing biological sequences in FASTA/FASTQ format
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atria-rs
running the Ablatio Triadum (ATria) centrality algorithm (Cickovski et al, 2015, 2017)
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intspan
Command line tools for IntSpan related bioinformatics operations
-
wdl-grammar
A parse tree for Workflow Description Language (WDL) documents
-
barbell
Extremely fast and accurate Nanopore demultiplexing
-
rust-bio-tools
A set of fast and robust command line utilities for bioinformatics tasks based on Rust-Bio
-
flow-plots
Package for drawing and interacting with plots in flow cytometry data
-
sigalign
A Similarity-Guided Alignment Algorithm
-
orphos-cli
Command-line interface for Orphos, a tool for finding protein-coding genes in microbial genomes
-
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…
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fastq-fix-i5
Rewrite FASTQ headers by reverse-complementing only the i5 (P5/index2) part in ...:i7+i5
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hgvs-weaver
High-performance HGVS variant mapping and validation engine
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kmerust
A fast, parallel k-mer counter for DNA sequences in FASTA and FASTQ files
-
voronota-ltr
Voronota-LT is an alternative version of Voronota for constructing tessellation-derived atomic contact areas and volumes
-
seqkmer
High-performance FASTA/FASTQ IO and minimizer-based k-mer analysis utilities for Rust bioinformatics pipelines
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sgcount
A fast and flexible sgRNA counter
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gdock
Fast information-driven protein-protein docking using genetic algorithms and physics-based scoring
-
kira-protein-pruner
High-performance protein analysis tools
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wdl-analysis
Analysis of Workflow Description Language (WDL) documents
-
noodles-vcf
Variant Call Format (VCF) reader and writer
-
librna-sys
Low-level bindings for the ViennaRNA library
-
oxbow
Read conventional genomic file formats as data frames and more via Apache Arrow
-
salti
A modern, fast, multiple sequence alignment browser - built for the terminal
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compact-genome
Representation of genomes
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fastars
Ultra-fast QC and trimming for short and long reads
-
gffx
An ultra-fast and memory-efficient toolkit for querying GFF files, written with Rust
-
bio-forge
A pure Rust library and CLI for the automated repair, preparation, and topology construction of biological macromolecules
-
fxtools
A collection of commandline Fasta/Fastq utility tools
-
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.
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wdl-format
Formatting of WDL (Workflow Description Language) documents
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pdbrust
A comprehensive Rust library for parsing and analyzing Protein Data Bank (PDB) files
-
kira-mmcif
Low-level, streaming mmCIF parser focused on protein coordinates
-
peacoqc-rs
PeacoQC quality control algorithms for flow cytometry
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htsget-http
handling HTTP in htsget-rs
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tgv
Explore genomes in the terminal. Light, blazing fast 🚀, vim-motion.
-
fasterp
High-performance FASTQ preprocessing tool - often faster than fastp with the same interface
-
twitcher
Find template switch mutations in genomic data
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sequenceprofiler
sequence similarity based on identity kmers and all sequence profiling under one rust crate
-
fastLoess
High-level, parallel LOESS (Locally Estimated Scatterplot Smoothing) implementation in Rust
-
parasail-rs
Rust bindings and wrapper for parasail, a SIMD C library for pairwise sequence alignment
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efficient_pca
Principal component computation using SVD and covariance matrix trick
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wham
weighted histogram analysis method
-
phylo
An extensible Phylogenetics library written in rust
-
flow-gates
Package for drawing and interacting with gates in flow cytometry data
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mbf-fastq-processor
The fast, reliable multitool of FASTQ processing
-
deacon
Fast DNA search and [host] depletion using minimizers
-
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
-
ARGenus
ARG detection and genus-level classification using flanking sequence analysis
-
biotools
bioinformatics CLI tools for sequence analysis and manipulation
-
wdl-doc
Documentation generator for Workflow Description Language (WDL) documents
-
rust_deseq2
A pure Rust implementation of DESeq2 for differential expression analysis of RNA-seq data
-
nohuman
Remove human reads from a sequencing run
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securiety
parsing and validating CURIE IDs
-
microBioRust
Microbiology friendly bioinformatics Rust functions
-
redicat
RNA Editing Cellular Assessment Toolkit: A highly parallelized utility for analyzing RNA editing events in single-cell RNA-seq data
-
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
-
haddock-restraints
Generate restraints to be used in HADDOCK
-
nafcodec
Rust coder/decoder for Nucleotide Archive Format (NAF) files
-
ref-solver
Solve reference genome identification from BAM/SAM headers
-
lightmotif-tfmpvalue
Rust reimplementation of TFMPvalue for the lightmotif crate
-
rebgzf
Efficient gzip to BGZF transcoder using Puffin-style half-decompression
-
ontology-registry
that lets you download, store and register ontologies
-
seqwish
A variation graph inducer - build pangenome graphs from pairwise alignments
-
single_rust
Single-cell analysis in Rust
-
sweepga
Efficient pangenome alignment filtering and sparsification tool
-
seq_io_parallel
A map-reduce style parallel extension to seq_io
-
ensemblcov
human genomics
-
noodles-csi
Coordinate-sorted index (CSI) format reader and writer
-
ska
Split k-mer analysis
-
odgi-ffi
A safe, ergonomic Rust wrapper for the odgi pangenome graph tool
-
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.
-
doiTAG
doiTAG for sequence DOIs
-
vcf-reformatter
Fast VCF file parser and reformatter with VEP and SnpEff annotation support which can output to MAF
-
noodles-bcf
Binary Call Format (BCF) reader and writer
-
wdl-lsp
Language Server Protocol implementation for WDL
-
atglib
handle transcripts for genomics and transcriptomics
-
wdl-engine
Execution engine for Workflow Description Language (WDL) documents
-
noodles-sam
Sequence Alignment/Map (SAM) format reader and writer
-
selexqc
High-performance parallel RNA Capture-SELEX library quality control
-
biodiff
Compare binary files using sequence alignment
-
sourmash
tools for comparing biological sequences with k-mer sketches
-
refman
A command-line manager for bespoke reference datasets used in bioinformatic analyses
-
libsais
Bindings to the C library libsais for suffix array construction
-
noodles-tabix
Tabix (TBI) format reader and writer
-
seq-hash
A SIMD-accelerated library to compute hashes of DNA sequences
-
slow5
interacting with slow5
-
fxread
A barebones fastx reader for rust
-
tsg
Deep Learning Processing Library for Biological Data
-
iitree-rs
Implicit augmented interval tree (IAITree/cgranges) with memory-mapped disk storage
-
rvdna
— AI-native genomic analysis and the .rvdna file format. Variant calling, protein prediction, and HNSW vector search in pure Rust with WASM support.
-
deepbiop
Deep Learning Processing Library for Biological Data
-
bamslice
Extract byte ranges from BAM files and convert to interleaved FASTQ format for parallel processing
-
orphos-core
Core library for Orphos, a tool for finding protein-coding genes in microbial genomes
-
thaf
Extracts transcript sequences and gene maps from genome FASTA files using GFF3 annotations
-
raxtax
k-mer-based non-Bayesian Taxonomic Classifier
-
noodles-cram
CRAM format reader and writer
-
rust-featurecounts
A fast feature counting tool for prokaryotic RNA-seq analysis, compatible with featureCounts
-
bgzip
Rust implementation of bgzip
-
nucleaze
Read filtering using k-mers
-
lightmotif-io
Parser implementations of several formats for the lightmotif crate
-
virust-splicing
High-performance command-line program for analyzing HIV-1 splicing patterns from NGS data
-
sketchlib
Genome and amino-acid sketching
-
minimap2-sys
Bindings to libminimap2
-
infer_sex
A high-performance, zero-dependency Rust library for inferring sex from variant data
-
fqtk
A toolkit for working with FASTQ files
-
tsg-cli
analyze and manipulate transcript segment graph (TSG)
-
nthash-rs
Pure‑Rust port of ntHash
-
htsget-test
Common test functions and utilities used by htsget-rs
-
bamnado
Tools and utilities for manipulation of BAM files for unusual use cases. e.g. single cell, MCC
-
genepred
port for the GenePred format in Rust
-
kira-protein-longevity-analysis
CLI tool for physics-informed protein robustness and fragility analysis under environmental conditions (pH, oxidative stress, temperature)
-
htsget-lambda
A cloud-based instance of htsget-rs using AWS Lambda, which serves data according to the htsget protocol
-
simd-sketch
A SIMD-accelerated library to compute a b-bit bottom-h sketch
-
crankshaft-monitor
Crankshaft monitor server
-
genedex
A small and fast FM-Index implementation
-
bsalign
Rust bindings for the bsalign C library
-
parfait-gfa
gfa v1/v2 parser and validator
-
noodles-util
noodles support utilities
-
bedrs
Genomic interval library in rust
-
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
-
coprosize
coprolite research (paleontology and archaeology): estimate the producer's body mass based on coprolite diameter by the use of regression models
-
xpclrs
A high-performance rust implementation of the XP-CLR method
-
pombase-gocam
Parser for Gene Ontology Consortium GO-CAM JSON files
-
fqgrep
Search a pair of fastq files for reads that match a given ref or alt sequence
-
noodles-gff
Generic Feature Format (GFF) reader and writer
-
kira-mitoqc
Deterministic mitochondrial QC scoring for single-cell expression matrices
-
noodles-bed
BED (Browser Extensible Data) reader and writer
-
kira-proteoqc
Deterministic, explainable proteostasis QC for single-cell expression data
-
crankshaft-config
Configuration facilities for Crankshaft
-
bgzf
working with explicitly BGZF compressed data
-
bsxplorer2
A high-performance library for bisulfite sequencing data analysis and DNA methylation research
-
rnapkin
CLI utility for drawing RNA secondary structure
-
phenopackets
Rust bindings for Phenopacket Schema
-
deepbiop-cli
CLI tool for Processing Biological Data
-
prseq
Rust tools (with Python bindings) for sequence analysis
-
fastqgen
Random paired fastq file generation. Nothing more, nothing less.
-
bam-builder
easily building BAMs for testing
-
pluma-plugin-trait
A trait defining the plugin interface for PluMA (Plugin-based Microbiome Analysis)
-
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…
-
consalifold
Consensus Secondary Structure Predictor Engaging Structural Alignment-based Error Correction
-
noodles-gtf
Gene Transfer Format (GTF) reader and writer
-
seqtable
High-performance parallel FASTA/FASTQ sequence counter
-
kira_cdh_compat_fastq_reader
Streaming FASTQ reader compatible with CD-HIT input handling (plain and .gz), safe idiomatic Rust API; sync and async
-
kira_cdh_compat_clstr
CD-HIT-compatible .clstr writer/reader and a semantic diff CLI
-
gia
set theoretic operations of genomic intervals
-
genome-graph
Representation of genome graphs
-
pa-types
Core library types for global pairwise alignment
-
fastq_rs
Multi purpose fastq toolkit
-
give_a_sheet
Toolkit for generating input samplesheets for a variety of nf-core pipelines
-
scidataflow
A command-line tool to manage scientific research project data
-
markov_genome
Learn the properties of a FASTA sequence database and simulate sequences in a Markov process
-
onecode
Rust bindings for ONEcode - a data representation format for genomic data
-
crankshaft-engine
The core engine that comprises Crankshaft
-
strobemers
A toolkit for generating strobemers
-
rna-ss-params
RNA secondary structure parameters
-
skope
Accelerated genome containment and abundance estimation
-
phylotree
deal with phylogenetic trees and distance matrices
-
biosynth
CLI: synthetic data generator for BioVault
-
disambiseq
Create unambiguous one-off mismatch libraries for DNA sequences
-
flash-cli
Command-line interface for the FLASH read merging algorithm
-
lightmotif-py
PyO3 bindings and Python interface to the lightmotif crate
-
genomicsqlite
Genomics Extension for SQLite
-
kamino-cli
Build phylogenomic datasets in seconds
-
nucleob
bioinformatics: nucleobases and amino acids statistics
-
hts-sys
HTSlib bindings
-
diced
reimplementation of the MinCED algorithm for identifying CRISPRs in full or assembled genomes
-
crankshaft-docker
Docker facilities for Crankshaft
-
placecare
A toolkit to quickly search for cis-acting regulatory elements using the PLACE database
-
dabuild
Access genome build metadata
-
microbiorust-py
Python bindings for microBioRust Microbiology friendly bioinformatics Rust functions
-
ragc-core
Core compression and decompression algorithms for the AGC genome compression format
-
minimizer-iter
Iterate over minimizers of a DNA sequence
-
kira_cdh_compat_cluster
Greedy clustering engine compatible with CD-HIT-like pipelines
-
wdl-cli
Facilities for building command-line tools using the
wdlcrates -
ebiotic
interacting with common bioinformatics web services
-
deepbiop-utils
Deep Learning Preprocessing Library for Biological Data
-
flow-tru-ols
TRU-OLS (Truncated ReUnmixing OLS) algorithm for flow cytometry unmixing
-
yacrd
Using all-against-all read mapping, yacrd performs: computation of pile-up coverage for each read and detection of chimeras
-
msafara
View, edit, and explore multiple sequence alignments in your terminal
-
pluma
Plugin Interface for Rust - provides FFI bindings and utilities for writing PluMA plugins in Rust
-
kira_cdh_compat_kmer_indexer
CD-HIT-compatible k-mer indexing (CD-HIT-NG) in Rust: fast, memory-efficient, mmap-ready
-
sais_drum
SAIS algorithm for suffix array construction
-
blutils-proc-adapter
easier to run and analyze Blast results
-
vcf
VCF Parser
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