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

wdl-ast

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

bio-seq

Bit packed and well-typed biological sequences

proseg

Probabilistic cell segmentation for in situ spatial transcriptomics

htsget-config

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

rasusa

Randomly subsample reads or alignments

lightmotif

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

bigtools

associated tools for reading and writing bigwigs and bigbeds

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

biotools

bioinformatics CLI tools for sequence analysis and manipulation

sequintools

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

tsg-cli

analyze and manipulate transcript segment graph (TSG)

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

predictosaurus

Uncertainty aware haplotype based genomic variant effect prediction

rust-lapper

A fast and easy interval overlap library

bsxplorer-ci

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

wdl-analysis

Analysis of Workflow Description Language (WDL) documents

cardio-rs

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

tsalign

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

sourmash

tools for comparing biological sequences with k-mer sketches

chemfiles

Modern library for chemistry trajectories reading and writing

lrge

Genome size estimation from long read overlaps

varfish-server-worker

Rust-based worker for varfish-server

fqkit

cross-platform program for fastq file manipulation

rustyms

handle proteomic mass spectrometry data and match peptides to spectra

seqsizzle

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

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

gb-io

parsing, writing and manipulating Genbank sequence files

hts-sys

HTSlib bindings

haddock-restraints

Generate restraints to be used in HADDOCK

mzsignal

mass spectrometry signal processing

openslide-rs

Rust bindings of OpenSlide C library

refman

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

sufr

Parallel Construction of Suffix Arrays in Rust

bed-reader

Read and write the PLINK BED format, simply and efficiently

genotype_cli

Genotype language CLI

plascad

PlasCAD

wdl-lint

Lint rules for Workflow Description Language (WDL) documents

htsget-axum

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

ontolius

A fast and safe crate for working with biomedical ontologies

fasten

A set of scripts to run basic analysis on fastq files

intspan

Command line tools for IntSpan related bioinformatics operations

finch

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

rust-bio-tools

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

KiThe

collection of structures and functions useful for chemical kinetics, chemical thermodynamics, combustion, heat and mass transfer, shock tubes and so on and so far. Work in progress…

pdbtbx

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

deacon

Fast alignment-free sequence filter

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

wham

weighted histogram analysis method

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.

tskit

rust interface to tskit

genome-graph

Representation of genome graphs

crispr_screen

A fast and configurable differential expression analysis tool for CRISPR screens

pombase-gocam

Parser for Gene Ontology Consortium GO-CAM JSON files

dnacomb

Count the occurances of structured sequence reads and compare to an expected library

rdkit

High level RDKit functionality for rust

slow5

interacting with slow5

chemical_elements

representing chemical compositions and generating isotopic patterns

coprosize

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

groan_rs

Gromacs Analysis Library for Rust

d4-hts

The htslib binding used by D4

scidataflow

A command-line tool to manage scientific research project data

lightmotif-py

PyO3 bindings and Python interface to the lightmotif crate

galah

Microbial genome dereplicator

minimap2-temp

Bindings to libminimap2

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.

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

fqgrep

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

exon

A platform for scientific data processing and analysis

light_phylogeny

Methods and functions for phylogeny

gskits

common kits

rust_abf

reading data from Axon Binary Format (ABF) files

genotype_lsp

Genotype language LSP server

fakit

program for fasta file manipulation

kmerutils

Kmer counting, hashing, sequence sketching

sigalign

A Similarity-Guided Alignment Algorithm

deepbiop-cli

CLI tool for Processing Biological Data

petgraph-graphml

GraphML output support for petgraph

fastlin

an ultra-fast program for MTBC lineage typing

oxinat

XNAT REST API client

check_build

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

mmft

A minimal fasta toolkit

paraseq

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

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

packed-seq

Constructing and iterating packed DNA sequences using SIMD

rustynetics

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

viguno

Phenotype/disease for VarFish

fastqc-rs

A fast quality control tool for FASTQ files written in rust

phylotree

deal with phylogenetic trees and distance matrices

rnapkin

CLI utility for drawing RNA secondary structure

phylo

An extensible Phylogenetics library written in rust

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…

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

cribtools

CLI for reading genome track files

gsetl

etl

nail

alignment inference tool

nwr

nwr is a command line tool for newick and taxonomy

parasail-rs

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

kseq

fasta/fastq format parser library

bitnuc

efficient nucleotide sequence manipulation using 2-bit encoding

smyl

Artificial Neuronal Network in Rust

bustools

Interacting with the kallisto/bus format of scRNAseq data

fastobo-owl

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

bcf_reader

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

seq-here

A fast tool for bio-sequence file processing

perbase

Fast and correct perbase BAM/CRAM analysis

coitrees

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

kbo-cli

Command-line interface to the kbo local aligner

bsalign

Rust bindings for the bsalign C library

righor

creates model of Ig/TCR sequences from sequencing data

genomers

Package to download NCBI genome data and metadata

consalifold

Consensus Secondary Structure Predictor Engaging Structural Alignment-based Error Correction

ska

Split k-mer analysis

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

klassify

Classify chimeric reads based on unique kmer contents

mzdeisotope

deisotope and charge state deconvolve mass spectra

finalspark-rs

live data recording from MEA devices

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…

iirs

Inverted repeats finder

librna-sys

Low-level bindings for the ViennaRNA library

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.

ggca

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

tidyvcf

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

fasta-stats

descriptive statistics on FASTA (biological sequence) data

compact-genome

Representation of genomes

ebiotic

interacting with common bioinformatics web services

raxtax

k-mer-based non-Bayesian Taxonomic Classifier

swc-neuron

CLI utility for interacting with SWC neuronal morphology files

d4-bigwig

The libBigWig binding used by D4

filterx_source

The source library for filterx

noodles-fasta

FASTA format reader and writer

barcode-count

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

asts

wdl-format

Formatting of WDL (Workflow Description Language) documents

hypermash

Genome/Metagenome sketching via HyperMinHash

extended-htslib

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

msgpass

Thin wrapper to a Message Passing Interface (MPI)

classeq-cli

A command line interface for the classeq library

syntesuite

TODO

wdl

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

biodivine-pbn-control

controlling parametrized Boolean networks

fastq-generator

A fastq generator for generation of synthetic fastq files

demes

specification

microBioRust

Microbiology friendly bioinformatics Rust functions

atglib

handle transcripts for genomics and transcriptomics

jseqio

Reading and writing biological sequences in FASTA or FASTQ format

forgers

VCF manipulation based on FORGe ranking

abpoa-rs

Rust bindings for abPOA: Adaptive Banded POA

haptk

Haplotype analysis toolkit

chem-eng-real-time-process-control-simulator

Process Control Library (Chemical Engineering) with real time transfer function simulators

ome_zarr_metadata

OME-Zarr (previously OME-NGFF) metadata

simd-sketch

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

codonrs

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

rosella

Metagenome assembled genome recovery from metagenomes using UMAP and HDBSCAN

libsufr

Parallel Construction of Suffix Arrays in Rust

bacdive

analyzer for microbial genomics

noodles-csi

Coordinate-sorted index (CSI) format reader and writer

pdbvis

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

exon-sdf

Exon SDF

scattr

estimating the copy number of large tandem repeats

crib

CLI for reading and writing genome track files

simpleaf

framework to make using alevin-fry even simpler

flowtigs

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

dihardts_omicstools

Collection of different omic tools, structs and enums

fastq

A parser for fastq

give_a_sheet

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

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

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.

mehari

Variant effect prediction all in Rust

seqalign

Sequence alignment using edit operations

dotnetrawfilereader-sys

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

mm2

minimap2 frontend

mikan-rs

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

taxonomy

Routines for loading, saving, and manipulating taxonomic trees

biodiff-align

Sequence alignment bindings for biodiff

genovo

Determine genes with significantly more mutations than expected by chance

convert-af

converting alevin-fry output to the AnnData format

kbo

Local alignment search with k-bounded matching statistics

coverm

Read coverage calculator for metagenomics

nanoq

Minimal but speedy quality control and summaries of nanopore reads

dtw_rs_band_fork

Fork of Dynamic Time Warping Library for Rust

interatomic

calculating inter-particle interactions

bird_tool_utils

Microbial genomics utility functions

genomicsqlite

Genomics Extension for SQLite

vcf

VCF Parser

rsvart

A small library for representing genomic variants and regions

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

htsget-test

Common test functions and utilities used by htsget-rs

fastxgz

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

lightmotif-tfmpvalue

Rust reimplementation of TFMPvalue for the lightmotif crate

lorikeet-genome

Strain resolver and variant caller via local reassembly for metagenomics

cheminee-similarity-model

Builds a Morgan fingerprint encoder model to accelerate similarity searches

fmlrc

FM-index Long Read Corrector - Rust implementation

seqkmer

sequence kmer

pdb-handler

functions to handle PDB files

nafcodec

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

bioformats-rs

Rust bindings of Bioformats Java library

tsg

Deep Learning Processing Library for Biological Data

bamrescue

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

gfatk

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

ncbitaxonomy

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

tf-binding-rs

Fast transcription factor binding site prediction and FASTA manipulation in Rust

fastax

Make phylogenetic trees and lineages from the NCBI Taxonomy database

mibig-taxa

NCBI taxdump handling for MIBiG

rsedlib

rust binding of edlib

nthash

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

chainsaw

manipulate newick trees

groslicer

Slice gro files by processing a stream of lines

boomphf-patched

Scalable and Efficient Minimal Perfect Hash Functions (version modified by Piotr Beling)

benchling

client, generated from the OpenAPI spec

seal

Needleman-Wunsch & Smith-Waterman sequence alignment

knuckles-parse

A tooklkit for parsing PDB records

lib3dmol

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

moleco

generate color swatches for chemical compounds

rna-ss-params

RNA secondary structure parameters

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

spikeq

A synthetic FASTQ record generator with pattern spiking

codenano-server

editing DNA molecular designs in a browser

phenotype-internal

Defines Phenotype trait for Peapod crate

exon-bigwig

Subcrate of the exon crate for working with BigWig files

filterx_info

The builtin function documentation library for filterx

bsxplorer2

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

obographs-dev

Load Obographs data files

bvreader

Reader for the BrainVision data format

tsgen

A random genome generator that generates template switches

rsabpoa

abpoa rust binding

flyteidl

Core Interface Definition for Flyte

na_seq

DNA and RNA sequence types and functions

ipac

Rust CLI to Install Igor Repositories

genotype_lang_py_tree

Genotype language Python target AST crate

nucleob

bioinformatics: nucleobases and amino acids statistics

orthanq

quantify haplotypes in an uncertainty-aware manner

chromsize

just get your chrom sizes

sbwt

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

frag_gene_scan_rs

gene prediction model for short and error-prone reads

bio-streams

Streaming bioinformatics data types

psylink

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

gfautil

Command line tools for working with GFA files and related formats

clade

phlyo tree, a phylogenetic tree construction software

bed-utils

manipulating genomic range objects

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…

msbwt2

multi-string BWT query library

seqdupes

Compress sequence duplicates

ecdna-lib

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

fire-fasta

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

align-cli

A command line interface for easily aligning sequences

simd-minimizers

A SIMD-accelerated library to compute random minimizers

jam-rs

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

fasta-cleaner

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

crankshaft-engine

The core engine that comprises Crankshaft

sumi

analysis for small RNA libraries with UMIs

tsg-btsg

analyze and manipulate transcript segment graph (TSG)

hyper-gen

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

thermolib

An open-source library for the calculation of fluid properties

chemcore

A cheminformatics toolkit

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

consprob

Quick Probability Inference Engine on RNA Structural Alignment

lightdock

Macromolecular docking software based on the GSO algorithm

elias_fano_rust

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

fpa_lr

fpa filter long read mapping information to save disk space

freesasa-sys

Rust raw FFI bindings for the freesasa C library

uniparc_xml_parser

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

bio-jtools

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

fastx

reads Fasta and FastQ files with little overhead

smafa

Read aligner for small pre-aligned sequences

distance_aa

A backend for the distAAnce web application

nohuman

Remove human reads from a sequencing run

diploid-contam-estimator

Estimating contamination level in diploid DNA seuqencing libraries

d4tools

The CLI utils for D4 file format

grass-runtime

Runtime library for GRASS

seqcol_rs

implement seqcol in rust

biofile

reading bioinformatics related files

mpileup

Pile up multiple bam files site by site

mni2mz3

Brain imaging surface mesh file format converter

noodles-vcf

Variant Call Format (VCF) reader and writer

alphabeta

Tools for analysing epigenetic data

bindashtree

MinHash based phylogenomics via neighbor joining

gchemol-gut

Selected utilities for Rust development

fasta-filter

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

oxbow

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

entrez-rs

Rust wrapper for the Entrez API

obofoundry

Structures to deserialize OBO Foundry listings into

bindash

One Permutation Hashing, Optimal Densification, Genomics

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

omics-variation

Foundational representations of variation in the Rust omics ecosystem

fxtools

A collection of commandline Fasta/Fastq utility tools

podders

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

drug-extraction-core

A core library for extracting drugs from text records

sprocket

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

chemical-formula

Chemical formula parser that can handle wt% and nested structure

winsfs-cli

Site frequency spectrum estimation based on window expectation-maximisation algorithm

genie-sys

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

xch-ceb

XCH - Chemical Equation Balancer

readfish-tools

Tools for analysing adaptive sampling data

bustools_cli

Rust reimplementation of bustools for scRNAseq processing

guide-counter

Fast and accurate guide counting for CRISPR screens

fusta

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

gfastats

GFA statistics

bamsalvage

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

vtracker

For tracking the relationship between group membership changes across versions

blobtk

Core utilities for BlobToolKit

seed_chain

A seeding and generic chaining mechanism for sequence-to-sequence alignment

grafen

Create graphene and other substrates for use in molecular dynamics simulations

filterx

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

nucleobases

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

sigalign-utils

utils for core

rustfastq

bare metal fastq parsing

bioform

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

sketchlib

Genome and amino-acid sketching

phenopackets

Rust bindings for Phenopacket Schema

gfa-reader

Reading gfa format v1

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

genotype_lang_ts_tree

Genotype language TypeScript target AST crate

pattern_partition_prediction

Reading and querying k-mer pattern partition information

maf2bed

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

sequence_domain

A DNA/RNA sequence domain

edlib_rs

interface to the C++ edlib library

diced

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

phenotypes

Common types and traits for modeling clinical information

thermorawfilereader

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

pyanndata

Rust APIs

ggetrs

Efficient querying of biological databases from the command line

gtdb_tree

parsing Newick format files, especially GTDB tree files

fastleng

read length statistics tool

secondary_rewriter

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

fasta

Tools for FASTA reading, writing and indexing

metaprofile

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

nwbview

Neurodata Without Borders viewer

optimigation

tools for evolutionary computation, participate GA

omics-coordinate

Foundational representations of coordinates in the Rust omics ecosystem

tsverify

Compare alignments produced by tsalign

fasta_windows

Make quick statistics in windows from a fasta file

prole

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

sfs-cli

Tools for working with site frequency spectra

libprosic

calling of genomic variants using a latent variable model

deepbiop-fq

Deep Learning Preprocessing Library for Fastq Format

mmap-bitvec

working with bit-vectors backed by memory-mapped files

debruijn

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

chemistru-elements

Basic Elemental Representation

census2csv

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

gtokenizers

tokenizing genomic data with an emphasis on region set data

feos

framework for equations of state and classical density functional theory

gfa

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

vcf_add_ids

Add IDs to VCF records

clstr

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

fqcat

rapidly merging FASTQ files. Never use cat again!

to-trans

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

noodles-bgzf

Blocked gzip format (BGZF) reader and writer

rust-parallelfastx

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

mzdeisotoper

Deisotoping and charge state deconvolution of mass spectrometry files

biodiff-wfa2-sys

Rust bindings for the WFA2 library

noodles-cram

CRAM format reader and writer

recmap

reading and working with recombination maps in Rust

rust-spoa

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

biogarden

A collection of basic bioinformatics algorithms

spoa

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

chembasics

Things for chemistry

read-structure

parsing and working with read structure descriptions

kmers

k-mer manipulation

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.

nii-rs

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

ambigviz

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

libnail

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

bio-io

My utilities for reading and writing bioinformatics file formats

fg-stitch-lib

Stitch aligner implementation and supporting utilities

uniprot

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

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)

seqrepo

Port of (read-only) functionality of biocommons/seqrepo to Rust

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。

msn-kit

CLI for working with Mass Spec data

microBioRust-seqmetrics

Microbiology friendly bioinformatics Rust functions

xdf

Read XDF Files

gdrs

GenomicDistributions package from bioconductor

seq_io_parallel

A map-reduce style parallel extension to seq_io

biotest

Generate random test data for bioinformatics

genotype_workspace

Genotype language workspace

slow5lib-sys

Low-level bindings to the slow5lib C library

grass-ir

IR for GRASS

enzymeml

The EnzymeML Rust library

psdm

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

exon-io

IO utilities for Exon

classeq-core

Core library for the classeq project

protein-translate

Translate nucleotide sequence to protein

proteinogenic

Chemical structure generation for protein sequences as SMILES string

fxread

A barebones fastx reader for rust

deepbiop-bam

Deep Learning Processing Library for Bam Format

rumi

PCR Deduplication via directional adjacency

ross

A set of scripts to run basic analysis on fastq files

cytos

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

kractor

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

libradicl

support library for alevin-fry

strif

identify interruptions in short tandem repeats across the genome

libwfa2

Bindings to the C implementation of WFA2-lib

jean_blosum

BLOSUM feature for jean

gia

set theoretic operations of genomic intervals

demes-forward-capi

C API to demes-forward crate

nu_plugin_bio

Parse and manipulate common bioinformatic formats in nushell

consprob-trained

Trainable Probability Inference Engine on RNA Structural Alignment

ehxacto

Find exact tandem repeat coordinates from approximate regions identified by ExpansionHunter denovo

noodles-gff

Generic Feature Format (GFF) reader and writer

liblrge

Genome size estimation from long read overlaps