Lib.rs

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.

needletail

FASTX parsing and k-mer methods

rust-htslib

HTSlib bindings and a high level Rust API for reading and writing BAM files

seq_io

Fast FASTA, FASTQ and FASTX parsing

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

minimap2

Bindings to libminimap2

google-genomics1-cli

A complete library to interact with genomics (protocol v1)

sgcount

A fast and flexible sgRNA counter

noodles

Bioinformatics I/O libraries

oarfish

A fast, accurate and versatile tool for long-read transcript quantification

bio-seq

Bit packed and well-typed biological sequences

proseg

Probabilistic cell segmentation for in situ spatial transcriptomics

rasusa

Randomly subsample reads or alignments

htsget-config

Used to configure htsget-rs by using a config file or reading environment variables

bigtools

associated tools for reading and writing bigwigs and bigbeds

lightmotif

A lightweight platform-accelerated library for biological motif scanning using position weight matrices

sequintools

A suite of tools for manipulating and reporting on NGS data that has sequins added to the sample

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

wdl-ast

An abstract syntax tree for Workflow Description Language (WDL) documents

biotools

bioinformatics CLI tools for sequence analysis and manipulation

atg

Convert transcripts between different file formats

grepq

quickly filter fastq files

verify-same-kmer-content

Verify that an SPSS has the same kmer content as a set of unitigs

gsearch

genome classification, probminhash hnsw, genome search

qwt

Quad Wavelet Tree

rust-lapper

A fast and easy interval overlap library

tsg-cli

analyze and manipulate transcript segment graph (TSG)

chemfiles

Modern library for chemistry trajectories reading and writing

sourmash

tools for comparing biological sequences with k-mer sketches

cardio-rs

computing heart rate variability (HRV) metrics from ECG and PPG data

tsalign

A sequence-to-sequence aligner that accounts for template switches

lrge

Genome size estimation from long read overlaps

varfish-server-worker

Rust-based worker for varfish-server

seqsizzle

A pager for viewing FASTQ files with fuzzy matching, allowing different adaptors to be colored differently

fqkit

cross-platform program for fastq file manipulation

rustyms

handle proteomic mass spectrometry data and match peptides to spectra

bsxplorer-ci

A high-performance tool for bisulfite sequencing data analysis and DNA methylation research

gb-io

parsing, writing and manipulating Genbank sequence files

fastobo

Faultless AST for Open Biomedical Ontologies

alevin-fry

A suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data

haddock-restraints

Generate restraints to be used in HADDOCK

openslide-rs

Rust bindings of OpenSlide C library

rust-bio-tools

A set of fast and robust command line utilities for bioinformatics tasks based on Rust-Bio

sufr

Parallel Construction of Suffix Arrays in Rust

refman

A command-line manager for bespoke reference datasets used in bioinformatic analyses

bed-reader

Read and write the PLINK BED format, simply and efficiently

genotype_cli

Genotype language CLI

plascad

PlasCAD

ontolius

A fast and safe crate for working with biomedical ontologies

mzpeaks

representing peaks in mass spectrometry data

hts-sys

HTSlib bindings

fasten

A set of scripts to run basic analysis on fastq files

finch

min-wise independent permutation locality sensitive hashing ('MinHashing') for genomic data and command-line utility for manipulation

intspan

Command line tools for IntSpan related bioinformatics operations

pdbtbx

open/edit/save (crystallographic) Protein Data Bank (PDB) and mmCIF files

wdl-analysis

Analysis of Workflow Description Language (WDL) documents

deacon

Fast alignment-free sequence filter

slow5

interacting with slow5

fqtk

A toolkit for working with FASTQ files

spiking_neural_networks

A package for designing and simulating biological neural network dynamics with neurotransmission

kun_peng

Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all

google-genomics1

A complete library to interact with genomics (protocol v1)

proteogenomics

protein genomics analyzers

wham

weighted histogram analysis method

genome-graph

Representation of genome graphs

tskit

rust interface to tskit

boomphf

Scalable and Efficient Minimal Perfect Hash Functions

pharmsol

solving analytic and ode-defined pharmacometric models

crispr_screen

A fast and configurable differential expression analysis tool for CRISPR screens

rdkit

High level RDKit functionality for rust

check_build

verify a VCF file against hg19 and hg38 references using a streaming, low-memory approach

coprosize

coprolite research (paleontology and archaeology): estimate the producer's body mass based on coprolite diameter by the use of regression models

d4-hts

The htslib binding used by D4

scidataflow

A command-line tool to manage scientific research project data

galah

Microbial genome dereplicator

pombase-gocam

Parser for Gene Ontology Consortium GO-CAM JSON files

minimap2-temp

Bindings to libminimap2

alignoth

creating alignment plots from bam files

phylodm

Efficient calculation of phylogenetic distance matrices

webgestalt

CLI for computing enrichment for different analytes using ORA, GSEA, or NTA

light_phylogeny

Methods and functions for phylogeny

exon

A platform for scientific data processing and analysis

fqgrep

Search a pair of fastq files for reads that match a given ref or alt sequence

rust_abf

reading data from Axon Binary Format (ABF) files

fastobo-owl

OWL language mapping for ontologies in the OBO flat file format 1.4

fakit

program for fasta file manipulation

packed-seq

Constructing and iterating packed DNA sequences using SIMD

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.

nail

alignment inference tool

phylotree

deal with phylogenetic trees and distance matrices

kmerutils

Kmer counting, hashing, sequence sketching

petgraph-graphml

GraphML output support for petgraph

fastqc-rs

A fast quality control tool for FASTQ files written in rust

fastlin

an ultra-fast program for MTBC lineage typing

seq-here

A fast tool for bio-sequence file processing

lightmotif-py

PyO3 bindings and Python interface to the lightmotif crate

oxinat

XNAT REST API client

mmft

A minimal fasta toolkit

paraseq

A minimal-copy parser for FASTA and FASTQ files built for paired parallel processing

wdl-lint

Lint rules for Workflow Description Language (WDL) documents

Fastatsplit

A modest program written in rust made to store wanted and unwanted FASTA sequences to different FASTA files. Born from the necessity to have a FASTA filtering tool faster than seqkit

rustynetics

A high-performance genomics libary specialized in handling BAM and BigWig files

rnapkin

CLI utility for drawing RNA secondary structure

genomers

Package to download NCBI genome data and metadata

deepbiop-cli

CLI tool for Processing Biological Data

phylo

An extensible Phylogenetics library written in rust

base_sequence_compression

compressing and decompressing DNA sequences

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…

sigalign

A Similarity-Guided Alignment Algorithm

hypermash

Genome/Metagenome sketching via HyperMinHash

gskits

common kits

gsetl

etl

kseq

fasta/fastq format parser library

parasail-rs

Rust bindings and wrapper for parasail, a SIMD C library for pairwise sequence alignment

htsget-actix

A webserver instance of htsget-rs using actix-web, which serves data according to the htsget protocol

bitnuc

efficient nucleotide sequence manipulation using 2-bit encoding

iirs

Inverted repeats finder

smyl

Artificial Neuronal Network in Rust

nwr

nwr is a command line tool for newick and taxonomy

kbo

Local alignment search with k-bounded matching statistics

bustools

Interacting with the kallisto/bus format of scRNAseq data

bcf_reader

a small, lightweight, pure-Rust library to allow efficient, cross-platform access to genotype data in BCF files

coitrees

A very fast data structure for overlap queries on sets of intervals

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

hamming_rs

Computes Hamming distance and weight -- if available and beneficial, uses a highly optimized avx2 implementation

perbase

Fast and correct perbase BAM/CRAM analysis

motif-scanner

Command line tool for scanning DNA sequences for transcription factor binding sites

mzdeisotope

deisotope and charge state deconvolve mass spectra

consalifold

Consensus Secondary Structure Predictor Engaging Structural Alignment-based Error Correction

righor

creates model of Ig/TCR sequences from sequencing data

ska

Split k-mer analysis

viguno

Phenotype/disease for VarFish

varlociraptor

calling of genomic variants using a latent variable model

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

dual_threshold_optimization

Dual Threshold Optimization compares two ranked lists of features (e.g. genes) to determine the rank threshold for each list that minimizes the hypergeometric p-value of the overlap of features…

finalspark-rs

live data recording from MEA devices

librna-sys

Low-level bindings for the ViennaRNA library

ggca

Computes efficiently the correlation (Pearson, Spearman or Kendall) and the p-value (two-sided) between all the pairs from two datasets

noodles-csi

Coordinate-sorted index (CSI) format reader and writer

gtars

Performance-critical tools to manipulate, analyze, and process genomic interval data. Primarily focused on building tools for geniml - our genomic machine learning python package.

swc-neuron

CLI utility for interacting with SWC neuronal morphology files

raxtax

k-mer-based non-Bayesian Taxonomic Classifier

compact-genome

Representation of genomes

ebiotic

interacting with common bioinformatics web services

klassify

Classify chimeric reads based on unique kmer contents

extended-htslib

extended HTSlib bindings and a high level Rust API for reading and writing BAM files

fasta-stats

descriptive statistics on FASTA (biological sequence) data

sequenceprofiler

sequence similarity based on identity kmers and all sequence profiling under one rust crate

filterx_source

The source library for filterx

noodles-fasta

FASTA format reader and writer

classeq-cli

A command line interface for the classeq library

syntesuite

TODO

biodivine-pbn-control

controlling parametrized Boolean networks

demes

specification

fastq-generator

A fastq generator for generation of synthetic fastq files

dotnetrawfilereader-sys

A low-level interface to a in-process dotnet runtime for Thermo Fisher's RawFileReader library

atglib

handle transcripts for genomics and transcriptomics

single_rust

Single-cell analysis in Rust

microBioRust

Microbiology friendly bioinformatics Rust functions

coverm

Read coverage calculator for metagenomics

RayBNN_Cell

Cell Position Generator for RayBNN

jseqio

Reading and writing biological sequences in FASTA or FASTQ format

tidyvcf

command-line tool to convert VCF files to tab/comma separated tables

asts

abpoa-rs

Rust bindings for abPOA: Adaptive Banded POA

rosella

Metagenome assembled genome recovery from metagenomes using UMAP and HDBSCAN

haptk

Haplotype analysis toolkit

ome_zarr_metadata

OME-Zarr (previously OME-NGFF) metadata

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.

simd-sketch

A SIMD-accelerated library to compute a b-bit bottom-h sketch

gfatk

command line tool for manipulating small to medium sized GFA files, and specifically for output from the genome assembler MBG

seqalign

Sequence alignment using edit operations

pdbvis

A 3D protein structure viewer that loads and visualizes proteins from the Protein Data Bank (PDB)

flowtigs

An algorithm for calculating flowtigs in a De Bruijn graph of DNA reads in metagenomes

simpleaf

framework to make using alevin-fry even simpler

d4-bigwig

The libBigWig binding used by D4

dihardts_omicstools

Collection of different omic tools, structs and enums

fastq

A parser for fastq

mikan-rs

A medical image kit for segmentation metrics evaluation, native Rust support, and Python bindings for cross-language performance

crib

CLI for reading and writing genome track files

scattr

estimating the copy number of large tandem repeats

yacrd

Using all-against-all read mapping, yacrd performs: computation of pile-up coverage for each read and detection of chimeras

sirius-bindings

Rust bindings for the SIRIUS metabolomics tool

voronota

Voronota-LT is an alternative version of Voronota for constructing tessellation-derived atomic contact areas and volumes

mm2

minimap2 frontend

vcf

VCF Parser

taxonomy

Routines for loading, saving, and manipulating taxonomic trees

exon-bigwig

Subcrate of the exon crate for working with BigWig files

kbo-cli

Command-line interface to the kbo local aligner

barcode-count

NGS barcode counter for DEL, CRISPR-seq, and Barcode-seq

genomicsqlite

Genomics Extension for SQLite

wdl-lsp

Language Server Protocol implementation for WDL

netview

mutual nearest neighbor graphs for genome-wide, fine-scale population structure determination and visualization

convert-af

converting alevin-fry output to the AnnData format

dtw_rs_band_fork

Fork of Dynamic Time Warping Library for Rust

hgvs

Port of biocommons/hgvs to Rust

nanoq

Minimal but speedy quality control and summaries of nanopore reads

noodles-vcf

Variant Call Format (VCF) reader and writer

nafcodec

Rust coder/decoder for Nucleotide Archive Format (NAF) files

rsvart

A small library for representing genomic variants and regions

generic_a_star

A generic implementation of the A* algorithm

fastxgz

A fasta/fastq parser for both compressed and not compressed files

codenano

editing DNA molecular designs

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.

grumpy

Genetic analysis in Rust

bird_tool_utils

Microbial genomics utility functions

tuni

Unify transcripts across different samples

gosh-model

Chemical model for gosh

give_a_sheet

Toolkit for generating input samplesheets for a variety of nf-core pipelines

filterx_info

The builtin function documentation library for filterx

lightmotif-tfmpvalue

Rust reimplementation of TFMPvalue for the lightmotif crate

lorikeet-genome

Strain resolver and variant caller via local reassembly for metagenomics

fmlrc

FM-index Long Read Corrector - Rust implementation

chromsize

just get your chrom sizes

pdb-handler

functions to handle PDB files

genovo

Determine genes with significantly more mutations than expected by chance

codonrs

Calculate relative synonymous codon usage for coding DNA sequences in a fasta file

genotype_lang_py_tree

Genotype language Python target AST crate

wu-diff

Compute differences between two slices using wu(the O(NP)) algorithm

bioformats-rs

Rust bindings of Bioformats Java library

bamrescue

check Binary Sequence Alignment / Map (BAM) files for corruption and repair them

tsg

Deep Learning Processing Library for Biological Data

ncbitaxonomy

Read NCBI Taxonomy Database from files and work with NCBI Taxonomy DB

mibig-taxa

NCBI taxdump handling for MIBiG

seal

Needleman-Wunsch & Smith-Waterman sequence alignment

rsabpoa

abpoa rust binding

seqkmer

sequence kmer

lib3dmol

written in rust to read, manipulate, select atoms in protein structure files

nthash

rolling hash function for hashing all possible k-mers in a DNA sequence

forgers

VCF manipulation based on FORGe ranking

groslicer

Slice gro files by processing a stream of lines

knuckles-parse

A tooklkit for parsing PDB records

benchling

client, generated from the OpenAPI spec

fastax

Make phylogenetic trees and lineages from the NCBI Taxonomy database

genomap

A small library for storing generic genomic data indexed by a chromosome

ontime

Extract subsets of ONT (Nanopore) reads based on time

minimap2-sys

Bindings to libminimap2

fastx

reads Fasta and FastQ files with little overhead

phenotype-internal

Defines Phenotype trait for Peapod crate

biodiff-align

Sequence alignment bindings for biodiff

bvreader

Reader for the BrainVision data format

na_seq

DNA and RNA sequence types and functions

obographs-dev

Load Obographs data files

bsxplorer2

A high-performance library for bisulfite sequencing data analysis and DNA methylation research

flyteidl

Core Interface Definition for Flyte

rna-ss-params

RNA secondary structure parameters

chainsaw

manipulate newick trees

bindashtree

MinHash based phylogenomics via neighbor joining

codenano-server

editing DNA molecular designs in a browser

aligner

Automatically corrects subtitle timings given a second correct subtitle

nucleob

bioinformatics: nucleobases and amino acids statistics

orthanq

quantify haplotypes in an uncertainty-aware manner

psylink

GUI for PsyLink neural interface for receiving/graphing biosignals and predicting user's intentions

bio-streams

Streaming bioinformatics data types

spikeq

A synthetic FASTQ record generator with pattern spiking

gfautil

Command line tools for working with GFA files and related formats

bed-utils

manipulating genomic range objects

d4tools

The CLI utils for D4 file format

centraldogma

client for Rust

finch_cli

min-wise independent permutation locality sensitive hashing ('MinHashing') for genomic data and command-line utility for manipulation

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…

seqdupes

Compress sequence duplicates

omics-coordinate

Foundational representations of coordinates in the Rust omics ecosystem

fire-fasta

Ultra-fast, lazy, zero-copy Multi-FASTA parser

ecdna-lib

The ecDNA distribution for the evolutionary of extra-chromosomal DNA (ecDNA)

frag_gene_scan_rs

gene prediction model for short and error-prone reads

sbwt

Indexing sets of DNA k-mers with the spectral Burrow-Wheeler transform

sumi

analysis for small RNA libraries with UMIs

clade

phlyo tree, a phylogenetic tree construction software

lib_tsshow

A visualiser for template-switch alignments

bindash

One Permutation Hashing, Optimal Densification, Genomics

fastleng

read length statistics tool

hyper-gen

HyperGen is a high-performance Rust library to sketch genomics files into hypervectors and realize fast Average Nucleotide Identity (ANI) approximation

jam-rs

Just another (genomic) minhash (Jam) implementation in Rust

blobtk

Core utilities for BlobToolKit

wdl

Lexing, parsing, validation, and linting for Workflow Description Language (WDL) documents

tsg-btsg

analyze and manipulate transcript segment graph (TSG)

chemcore

A cheminformatics toolkit

lightdock

Macromolecular docking software based on the GSO algorithm

crussmap

faster tool to convert genome coordinates between difference reference assemblies. Support file formats: [BED,…]. This project reconstructs the CrossMap…

rustbam

Rust-powered BAM depth extraction with Python bindings

elias_fano_rust

An optimized implementation of Sebastiano Vigna's Elis-Fano quasi succint datastructure

dag-scheduler

a scheduler of dag computation graph

obofoundry

Structures to deserialize OBO Foundry listings into

uniparc_xml_parser

Scripts for parsing UniParc XML files downloaded from the Uniprot website into CSV files

smafa

Read aligner for small pre-aligned sequences

nohuman

Remove human reads from a sequencing run

bio-jtools

A suite of bioinformatics tools for interacting with high throughput sequencing (HTS) data

diploid-contam-estimator

Estimating contamination level in diploid DNA seuqencing libraries

simd-minimizers

A SIMD-accelerated library to compute random minimizers

fpa_lr

fpa filter long read mapping information to save disk space

freesasa-sys

Rust raw FFI bindings for the freesasa C library

mpileup

Pile up multiple bam files site by site

seqcol_rs

implement seqcol in rust

biofile

reading bioinformatics related files

consprob

Quick Probability Inference Engine on RNA Structural Alignment

mni2mz3

Brain imaging surface mesh file format converter

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

podders

Write uncompressed Pod5 files in native rust. No FFI! PODDDDERS

fxtools

A collection of commandline Fasta/Fastq utility tools

openslide-sys

Low-level bindings to the openslide library

diced

reimplementation of the MinCED algorithm for identifying CRISPRs in full or assembled genomes

oxbow

Read specialized bioinformatic file formats as data frames in R, Python, and more

winsfs-cli

Site frequency spectrum estimation based on window expectation-maximisation algorithm

genotype_lang_ts_tree

Genotype language TypeScript target AST crate

entrez-rs

Rust wrapper for the Entrez API

align-cli

A command line interface for easily aligning sequences

fasta-filter

Filter a FASTA file and output a subset of the records on STDOUT

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.

webgestalt_lib

computing enrichment for different analytes using ORA or GSEA

filterx

A command line tool to filter data by using python-like syntax

fasta-cleaner

Transform fasta files by upper-casing all sequence characters and removing non-ACGT sequence characters

genie-sys

binding for Genie (A Open Source MPEG-G Codec)

alphabeta

Tools for analysing epigenetic data

drug-extraction-core

A core library for extracting drugs from text records

pyanndata

Rust APIs

thermorawfilereader

A (relatively) high level interface to Thermo Fisher's RawFileReader library

guide-counter

Fast and accurate guide counting for CRISPR screens

phenopackets

Rust bindings for Phenopacket Schema

gfastats

GFA statistics

genotype_lang_py_config

Genotype language Python target config crate

bamsalvage

Rust version of bamsalvage, retrieving sequences from a corrupted BAM file as much as possible

libnail

that performs profile Hidden Markov Model (PHMM) biological sequence alignment

bustools_cli

Rust reimplementation of bustools for scRNAseq processing

readfish-tools

Tools for analysing adaptive sampling data

grafen

Create graphene and other substrates for use in molecular dynamics simulations

nucleobases

low-level brick crate for managing nucleobases as data in code

bioform

Tools for sniffing, parsing, and manipulating common biological file formats

rustfastq

bare metal fastq parsing

mzdeisotoper

Deisotoping and charge state deconvolution of mass spectrometry files

sketchlib

Genome and amino-acid sketching

gfa-reader

Reading gfa format v1

sequence_domain

A DNA/RNA sequence domain

pattern_partition_prediction

Reading and querying k-mer pattern partition information

llvm-scratch

Free Standing library in Rust

maf2bed

Converts multiple alignment format (MAF) files to a BED format for tabixing. Used with jbrowse-plugin-mafviewer

genominicus

plot gene trees

prole

collection of re-usable methods in Rust. Feel free to use them for your own work.

libprosic

calling of genomic variants using a latent variable model

noodles-cram

CRAM format reader and writer

rspoa

A POA implementation in Rust

ggetrs

Efficient querying of biological databases from the command line

biodiff-wfa2-sys

Rust bindings for the WFA2 library

graphannis-core

supports graph representation and generic query-functionality

bio-io

My utilities for reading and writing bioinformatics file formats

nwbview

Neurodata Without Borders viewer

metaprofile

Segregate WGS data into windows along the genome. Optionally, run tools such as alphabeta for each window.

fasta

Tools for FASTA reading, writing and indexing

optimigation

tools for evolutionary computation, participate GA

wdl-format

Formatting of WDL (Workflow Description Language) documents

fusta

leverages the FUSE interface to transparently manipulate multiFASTA files as independent files

fasta_windows

Make quick statistics in windows from a fasta file

sfs-cli

Tools for working with site frequency spectra

sigalign-utils

utils for core

deepbiop-fq

Deep Learning Preprocessing Library for Fastq Format

secondary_rewriter

Adds SEQ and QUAL fields to secondary alignments from the primary alignment

mmap-bitvec

working with bit-vectors backed by memory-mapped files

census2csv

Convert TMT multiplexed proteomics data in the Census format to CSV files

debruijn

Tools for DNA sequences: efficient k-mer manipulation, De Bruijn graph construction and compaction and handling of DNA strings

gfa

working with graphs in the GFA (Graphical Fragment Assembly) format

genotype

An abstraction layer between genotype and phenotype, with in-place mutation

tsgen

A random genome generator that generates template switches

edlib_rs

interface to the C++ edlib library

biogarden

A collection of basic bioinformatics algorithms

gtdb_tree

parsing Newick format files, especially GTDB tree files

to-trans

A high-performance transcriptome builder from fasta + GTF/GFF

mehari

Variant effect prediction all in Rust

gtokenizers

tokenizing genomic data with an emphasis on region set data

rust-parallelfastx

Parallel iteration of FASTA/FASTQ files, for when sequence order doesn't matter but speed does

recmap

reading and working with recombination maps in Rust

chainfile

working with genomics chain files

rust-spoa

wraps the C++ SPOA library for generating DNA and protein consensus sequences

microBioRust-seqmetrics

Microbiology friendly bioinformatics Rust functions

bacdive

analyzer for microbial genomics

spoa

wrapper around the spoa C++ SIMD partial order alignment library

read-structure

parsing and working with read structure descriptions

nii-rs

reading/writing NIfTI files, with SimpleITK/Nibabel-like APIs, native Rust support, and Python bindings for cross-language performance

kmers

k-mer manipulation

msn-kit

CLI for working with Mass Spec data

uniprot

Rust data structures and parser for the Uniprot database(s)

hts

Rust binding for htslib

xdrfile

Wrapper around the gromacs libxdrfile library. Can be used to read and write gromacs trajectories in xtc and trr format.

kinesin

re-exports crate (WIP)

exon-sam

Exon SAM

bio-rust

解析生物信息领域的基本数据结构，提供操纵这些数据的接口和构建一些统计模型。

cytos

A collection of frequently used Bioinformatics scripts/tasks written in Rust

fg-stitch-lib

Stitch aligner implementation and supporting utilities

xdf

Read XDF Files

ngs

Command line tool for processing next-generation sequencing data

packet-9dfd7e7b6ae4d549987171c9f89a823d

experiment

seq_io_parallel

A map-reduce style parallel extension to seq_io

fqcat

rapidly merging FASTQ files. Never use cat again!

ambigviz

Identify and plot ambiguous nucleotide bases at given positions from a BAM file

biotest

Generate random test data for bioinformatics

gdrs

GenomicDistributions package from bioconductor

slow5lib-sys

Low-level bindings to the slow5lib C library

deepbiop-bam

Deep Learning Processing Library for Bam Format

grass-runtime

Runtime library for GRASS

enzymeml

The EnzymeML Rust library

lorikeet-rs

Strain resolver for metagenomics

psdm

Compute a pairwise SNP distance matrix from one or two alignment(s)

distance_aa

A backend for the distAAnce web application

exon-io

IO utilities for Exon

sprocket

A command line tool for working with Workflow Description Language (WDL) files

fxread

A barebones fastx reader for rust

protein-translate

Translate nucleotide sequence to protein

proteinogenic

Chemical structure generation for protein sequences as SMILES string

kractor

Extract reads from a FASTQ file based on taxonomic classification via Kraken2

nu_plugin_bio

Parse and manipulate common bioinformatic formats in nushell

rumi

PCR Deduplication via directional adjacency

ross

A set of scripts to run basic analysis on fastq files

clstr

parse and write .clstr files from 'CD-HIT', as well as a small binary with simple functionality

libradicl

support library for alevin-fry

census-proteomics

working with proteomics data quantified by the Census algorithm

grass-ir

IR for GRASS

gia

set theoretic operations of genomic intervals

jean_blosum

BLOSUM feature for jean

noodles-gff

Generic Feature Format (GFF) reader and writer

noodles-fastq

FASTQ format reader and writer

demes-forward-capi

C API to demes-forward crate

phenopackets-dev

Rust bindings for Phenopacket Schema

classeq-core

Core library for the classeq project