Lib.rs

needletail

FASTX parsing and k-mer methods

rust-htslib

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

oarfish

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

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

atg

Convert transcripts between different file formats

minimap2

Bindings to libminimap2

sgcount

A fast and flexible sgRNA counter

bio-seq

Bit packed and well-typed biological sequences

varfish-server-worker

Rust-based worker for varfish-server

proseg

Probabilistic cell segmentation for in situ spatial transcriptomics

lightmotif

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

grepq

quickly filter fastq files

sourmash

tools for comparing biological sequences with k-mer sketches

noodles

Bioinformatics I/O libraries

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

predictosaurus

Uncertainty aware haplotype based genomic variant effect prediction

lrge

Genome size estimation from long read overlaps

haddock-restraints

Generate restraints to be used in HADDOCK

rust-lapper

A fast and easy interval overlap library

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.

rust-bio-tools

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

alevin-fry

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

fastobo

Faultless AST for Open Biomedical Ontologies

rustyms

handle proteomic mass spectrometry data and match peptides to spectra

gsetl

etl

cardio-rs

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

hgvs

Port of biocommons/hgvs to Rust

rasusa

Randomly subsample reads or alignments

wdl-analysis

Analysis of Workflow Description Language (WDL) documents

tes

working with the Task Execution Service (TES) specification

seqsizzle

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

bed-reader

Read and write the PLINK BED format, simply and efficiently

plascad

PlasCAD

biotools

bioinformatics CLI tools for sequence analysis and manipulation

verify-same-kmer-content

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

hts-sys

HTSlib bindings

sufr

Parallel Construction of Suffix Arrays in Rust

fqkit

cross-platform program for fastq file manipulation

finch

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

fasten

A set of scripts to run basic analysis on fastq files

sequenceprofiler

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

pdbtbx

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

intspan

Command line tools for IntSpan related bioinformatics operations

ontolius

A fast and safe crate for working with biomedical ontologies

deacon

Fast alignment-free sequence filter

genome-graph

Representation of genome graphs

fqtk

A toolkit for working with FASTQ files

rdkit

High level RDKit functionality for rust

slow5

interacting with slow5

kun_peng

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

coprosize

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

mzdeisotope

deisotope and charge state deconvolve mass spectra

crispr_screen

A fast and configurable differential expression analysis tool for CRISPR screens

d4-hts

The htslib binding used by D4

exon

A platform for scientific data processing and analysis

wdl

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

scidataflow

A command-line tool to manage scientific research project data

galah

Microbial genome dereplicator

alignoth

creating alignment plots from bam files

viguno

Phenotype/disease for VarFish

packed-seq

Constructing and iterating packed DNA sequences using SIMD

give_a_sheet

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

sigalign

A Similarity-Guided Alignment Algorithm

hypermash

Genome/Metagenome sketching via HyperMinHash

light_phylogeny

Methods and functions for phylogeny

proteogenomics

protein genomics analyzers

extended-htslib

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

phylotree

deal with phylogenetic trees and distance matrices

spiking_neural_networks

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

rnapkin

CLI utility for drawing RNA secondary structure

phylo

An extensible Phylogenetics library written in rust

fakit

program for fasta file manipulation

varlociraptor

calling of genomic variants using a latent variable model

genomers

Package to download NCBI genome data and metadata

lightmotif-py

PyO3 bindings and Python interface to the lightmotif crate

mmft

A minimal fasta toolkit

minimap2-temp

Bindings to libminimap2

seq-here

A fast tool for bio-sequence file processing

rustynetics

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

fastqc-rs

A fast quality control tool for FASTQ files written in rust

fastlin

an ultra-fast program for MTBC lineage typing

fqgrep

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

kmerutils

Kmer counting, hashing, sequence sketching

nail

alignment inference tool

gskits

common kits

librna-sys

Low-level bindings for the ViennaRNA 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

parasail-rs

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

nwr

nwr is a command line tool for newick and taxonomy

consalifold

Consensus Secondary Structure Predictor Engaging Structural Alignment-based Error Correction

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

perbase

Fast and correct perbase BAM/CRAM analysis

ebiotic

interacting with common bioinformatics web services

cribtools

CLI for reading genome track files

fasta-stats

descriptive statistics on FASTA (biological sequence) data

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…

fastq-generator

A fastq generator for generation of synthetic fastq files

ggca

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

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

bindash

One Permutation Hashing, Optimal Densification, Genomics

finalspark-rs

live data recording from MEA devices

classeq-cli

A command line interface for the classeq library

atglib

handle transcripts for genomics and transcriptomics

ska

Split k-mer analysis

scattr

estimating the copy number of large tandem repeats

klassify

Classify chimeric reads based on unique kmer contents

forgers

VCF manipulation based on FORGe ranking

mikan-rs

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

refman

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

righor

creates model of Ig/TCR sequences from sequencing data

compact-genome

Representation of genomes

coverm

Read coverage calculator for metagenomics

genominicus

plot gene trees

d4-bigwig

The libBigWig binding used by D4

syntesuite

TODO

gfatk

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

abpoa-rs

Rust bindings for abPOA: Adaptive Banded POA

microBioRust

Microbiology friendly bioinformatics Rust functions

jseqio

Reading and writing biological sequences in FASTA or FASTQ format

bio-read

Bionic reading in terminal

mm2

minimap2 frontend

noodles-cram

CRAM format reader and writer

omics-variation

Foundational representations of variation in the Rust omics ecosystem

simpleaf

framework to make using alevin-fry even simpler

haptk

Haplotype analysis toolkit

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

rosella

Metagenome assembled genome recovery from metagenomes using UMAP and HDBSCAN

genovo

Determine genes with significantly more mutations than expected by chance

exon-bigwig

Subcrate of the exon crate for working with BigWig files

ome_zarr_metadata

OME-Zarr (previously OME-NGFF) metadata

chromsize

just get your chrom sizes

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.

asts

fastq

A parser for fastq

yacrd

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

simd-minimizers

A SIMD-accelerated library to compute random minimizers

taxonomy

Routines for loading, saving, and manipulating taxonomic trees

lib_tsalign

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

diced

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

rsvart

A small library for representing genomic variants and regions

filterx_engine

The engine library for filterx

dihardts_omicstools

Collection of different omic tools, structs and enums

fire-fasta

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

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.

sprocket

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

thermorawfilereader

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

na_seq

DNA and RNA sequence types and functions

lorikeet-genome

Strain resolver and variant caller via local reassembly for metagenomics

exon-sdf

Exon SDF

spikeq

A synthetic FASTQ record generator with pattern spiking

obographs-dev

Load Obographs data files

ncbitaxonomy

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

mehari

Variant effect prediction all in Rust

knuckles-parse

A tooklkit for parsing PDB records

blobtk

Core utilities for BlobToolKit

fastax

Make phylogenetic trees and lineages from the NCBI Taxonomy database

bird_tool_utils

Microbial genomics utility functions

pdb-handler

functions to handle PDB files

ontime

Extract subsets of ONT (Nanopore) reads based on time

convert-af

converting alevin-fry output to the AnnData format

nthash

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

seqkmer

sequence kmer

orthanq

quantify haplotypes in an uncertainty-aware manner

genomap

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

dabuild

Access genome build metadata

nucleob

bioinformatics: nucleobases and amino acids statistics

seqdupes

Compress sequence duplicates

omics-coordinate

Foundational representations of coordinates in the Rust omics ecosystem

fasta-filter

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

fmlrc

FM-index Long Read Corrector - Rust implementation

bindashtree

MinHash based phylogenomics via neighbor joining

bio-streams

Streaming bioinformatics data types

align-cli

A command line interface for easily aligning sequences

seed_chain

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

grumpy

Genetic analysis in Rust

rna-ss-params

RNA secondary structure parameters

codenano-server

editing DNA molecular designs in a browser

flyteidl

Core Interface Definition for Flyte

psylink

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

msbwt2

multi-string BWT query library

seal

Needleman-Wunsch & Smith-Waterman sequence alignment

jam-rs

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

bacdive

analyzer for microbial genomics

sumi

analysis for small RNA libraries with UMIs

fpa_lr

fpa filter long read mapping information to save disk space

ecdna-lib

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

fxtools

A collection of commandline Fasta/Fastq utility tools

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

gfautil

Command line tools for working with GFA files and related formats

minimap2-sys

Bindings to libminimap2

bvreader

Reader for the BrainVision data format

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…

gannot

A small library with limited functionality focused on genome annotation

nohuman

Remove human reads from a sequencing run

bed-utils

manipulating genomic range objects

finch_cli

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

fastxgz

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

demes-forward-capi

C API to demes-forward crate

mni2mz3

Brain imaging surface mesh file format converter

lib3dmol

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

chainsaw

manipulate newick trees

chainfile

working with genomics chain files

nii-rs

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

elias_fano_rust

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

noodles-tabix

Tabix (TBI) format reader and writer

fastleng

read length statistics tool

mzdeisotoper

Deisotoping and charge state deconvolution of mass spectrometry files

biofile

reading bioinformatics related files

ggetrs

Efficient querying of biological databases from the command line

frag_gene_scan_rs

gene prediction model for short and error-prone reads

distance_aa

A backend for the distAAnce web application

podders

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

simd-sketch

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

oxbow

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

heme

PDB reader and other protein modeling tools

gchemol-lattice

Periodic 3D crystal lattice

biodiff-wfa2-sys

Rust bindings for the WFA2 library

consprob

Quick Probability Inference Engine on RNA Structural Alignment

strif

identify interruptions in short tandem repeats across the genome

prole

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

diploid-contam-estimator

Estimating contamination level in diploid DNA seuqencing libraries

uniprot

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

hmmsearch_rs

gene prediction, Hidden Markov models

seqrepo

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

bio-jtools

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

xdrfile

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

drug-extraction-core

A core library for extracting drugs from text records

entrez-rs

Rust wrapper for the Entrez API

lightdock

Macromolecular docking software based on the GSO algorithm

nwbview

Neurodata Without Borders viewer

bustools_cli

Rust reimplementation of bustools for scRNAseq processing

classeq-api

API for Classeq

filterx_info

The builtin function documentation library for filterx

libdrugplotter

Easily compute drug concentration curves

bamrescue

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

slow5lib-sys

Low-level bindings to the slow5lib C library

nucleobases

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

gdrs

GenomicDistributions package from bioconductor

rustfastq

bare metal fastq parsing

rust-ena

ena-crate interacts directly with the European Nucleotide Archive(ENA)

mmap-bitvec

working with bit-vectors backed by memory-mapped files

tsgen

A random genome generator that generates template switches

ppgg

associated executable, the library provides tools for building tools that can parse and work for VCF and FASTA files while the associated executable is a command line tool for generating…

noodles-gff

Generic Feature Format (GFF) reader and writer

fusta

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

crib

CLI for reading and writing genome track files

wdl-grammar

A parse tree for Workflow Description Language (WDL) documents

seq_io_parallel

A map-reduce style parallel extension to seq_io

psdm

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

recmap

reading and working with recombination maps in Rust

fasta_windows

Make quick statistics in windows from a fasta file

rumi

PCR Deduplication via directional adjacency

sigalign-utils

utils for core

sfs-cli

Tools for working with site frequency spectra

phenopackets-dev

Rust bindings for Phenopacket Schema

gfa

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

microBioRust-seqmetrics

Microbiology friendly bioinformatics Rust functions

census-proteomics

working with proteomics data quantified by the Census algorithm

biotest

Generate random test data for bioinformatics

tsg-core

analyze and manipulate transcript segment graph (TSG)

msn-kit

CLI for working with Mass Spec data

chem-parse

A parser for simple chemical forumulas

sketchlib

Genome and amino-acid sketching

ffforf

fasta/q/x file format parser. Well fuzzed.

genotype

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

gfacut

Cutting out parts of the genome

rustbam

Rust-powered BAM depth extraction with Python bindings

mutexpect

functions for determining potential point mutations in a genetic sequence and their statisical probability

to-trans

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

exon-io

IO utilities for Exon

rust-parallelfastx

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

hyper-gen

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

sequence_domain

A DNA/RNA sequence domain

biostats

A bioinformatics library

hmmer-rs-2

Ergonomic Rust interface to HMMER

guide-counter

Fast and accurate guide counting for CRISPR screens

fxread

A barebones fastx reader for rust

cytos

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

libwfa2

Bindings to the C implementation of WFA2-lib

mpileup

Pile up multiple bam files site by site

kinesin

re-exports crate (WIP)

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。

freesasa-sys

Rust raw FFI bindings for the freesasa C library

grass-runtime

Runtime library for GRASS

kractor

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

diced-py

PyO3 bindings and Python interface to the diced crate

efetch2jsonl

Convert EFetch XML to JSON Lines

gkl

Genomics Kernel Library

sorensen

Sørensen–Dice coefficient implementation for Rust

genie-sys

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

gfastats

GFA statistics

primaldimer_rs

calculating PrimerPrimer interactions

ngs

Command line tool for processing next-generation sequencing data

read-structure

parsing and working with read structure descriptions

genome

package used to generate DNA used for GAN generator

libradicl

support library for alevin-fry

libnail

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

ehxacto

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

psychophysics

psychophysical experiments

tsg-cli

analyze and manipulate transcript segment graph (TSG)

lorikeet-rs

Strain resolver for metagenomics

bedblocks

Split a BED file into blocks

lightmotif-tfmpvalue

Rust reimplementation of TFMPvalue for the lightmotif crate

exon-fcs

Exon FCS

edlib_rs

interface to the C++ edlib library

pilercr-parser

A parser for the output of the PILER-CR CRISPR array annotation tool

consprob-trained

Trainable Probability Inference Engine on RNA Structural Alignment

ross

A set of scripts to run basic analysis on fastq files

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.

fasta_split

Split a fasta file into several fasta files

aa-regex

macros to build regular expression matching protein sequences

granges

command line tool for genomic range operations

filterx_source

The source library for filterx

mzsvg

draw mass spectra

fastix

prefix renaming FASTA records

chiral-common

Common Stuff of Chiral: An All-in-One Data Processing Tool

gia

set theoretic operations of genomic intervals

phcue-ck

command line tool to obtain FTP links to FASTQ files from ENA using run accession

biosignal

processing biological signals

ambigviz

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

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.

gffkit

program for gff3 file manipulation

fastx-statistics

Compute simple statistics for fasta-like files

mzdeisotope-map

deisotope and charge state deconvolve mass spectra

omics-molecule

Foundational representations of biological molecules in the Rust omics ecosystem

libparasail-sys

Unsafe Rust bindings for the parasail C library

census2csv

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

crispr

designing sgRNAs for genome engineering using CRISPR/Cas9

rust-seq2kminmers

Construction and iteration of k-min-mers from a DNA sequence

pattern_partition_prediction

Reading and querying k-mer pattern partition information

bamsalvage

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

libprosic

calling of genomic variants using a latent variable model

protein-translate

Translate nucleotide sequence to protein

rosalind-cli

CLI for rosalind crate

check_build

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

biogarden

A collection of basic bioinformatics algorithms

alphabeta

Tools for analysing epigenetic data

pubchem

Rust data structures and client for the PubChem API

grass-ir

IR for GRASS

jean_blosum

BLOSUM feature for jean

crispr_helloworld

Hello world project

wham

weighted histogram analysis method

metaprofile

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

protein

Working with protein structures

phenopackets

Rust bindings for Phenopacket Schema

GetPDB

Download Protein files from rcsb.org

rust-spoa

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

omnitigs

Omnitig-related algorithms

consalign

RNA Structural Aligner Based on Transfer-learning and Thermodynamic Ensemble Model

ncbi

Rust data structures for NCBI APIs

bedrs

Genomic interval library in rust

classeq-core

Core library for the classeq project

ncbi_dl

download ncbi genome file

noodles-util

noodles support utilities

sdust

symmetric DUST algorithm, with optional CLI

gsearch

genome classification, probminhash hnsw, genome search

handlegraph

in variation graphs

unitig_flipper

Reorienting unitigs to reduce the number of dummy nodes in an SBWT

bigsig

Large-scale Sequence Search with BItsliced Genomic Signature Index (BIGSIG)

vcfverifier

Verifies that a given VCF matches a given FASTA by comparing the REF column in the VCF to the underlying FASTA sequences

saboten

biedged graphs, cactus graphs and trees, and an algorithm for finding ultrabubbles in variation graphs

abpoa-sys

Automatically generated FFI definitions for abPOA

bitnuc-mismatch

Create unambiguous one-off mismatch hash tables from bitnuc scalars

prot_translate

Translate nucleotide sequence to protein

drprg

Drug resistance prediction with reference graphs

aa_similarity

Substitution matrices for use in protein sequence analysis and alignment