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

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

seq_io

Fast FASTA, FASTQ and FASTX parsing

minimap2

Bindings to libminimap2

google-genomics1-cli

A complete library to interact with genomics (protocol v1)

sgcount

A fast and flexible sgRNA counter

wdl-ast

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

rust-bio-tools

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

noodles

Bioinformatics I/O libraries

bio-seq

Bit packed and well-typed biological sequences

simpleaf

framework to make using alevin-fry even simpler

rasusa

Randomly subsample reads or alignments

rustyms

handle proteomic mass spectrometry data and match peptides to spectra

lightmotif

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

proseg

Probabilistic cell segmentation for in situ spatial transcriptomics

align-cli

A command line interface for easily aligning sequences

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

sequintools

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

biotools

bioinformatics CLI tools for sequence analysis and manipulation

atg

Convert transcripts between different file formats

annonars

Genome annotation based on Rust and RocksDB

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

rust-lapper

A fast and easy interval overlap library

bigtools

associated tools for reading and writing bigwigs and bigbeds

grepq

quickly filter fastq files

bsxplorer-ci

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

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.

sufr

Parallel Construction of Suffix Arrays in Rust

bqtools

A command-line tool for interacting with BINSEQ file formats

kractor

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

wdl-lint

Lint rules for Workflow Description Language (WDL) documents

lrge

Genome size estimation from long read overlaps

sourmash

tools for comparing biological sequences with k-mer sketches

fqkit

cross-platform program for fastq file manipulation

chemfiles

Modern library for chemistry trajectories reading and writing

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…

genotype_cli

Genotype language CLI

fasten

A set of scripts to run basic analysis on fastq files

fastobo

Faultless AST for Open Biomedical Ontologies

haddock-restraints

Generate restraints to be used in HADDOCK

seqsizzle

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

mzsignal

mass spectrometry signal processing

oarfish

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

cardio-rs

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

plascad

PlasCAD

bed-reader

Read and write the PLINK BED format, simply and efficiently

refman

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

slim-runner

Run SLiM simulation grid runs in parallel

deepbiop-cli

CLI tool for Processing Biological Data

nwr

nwr is a command line tool for newick and taxonomy

gb-io

parsing, writing and manipulating Genbank sequence files

hts-sys

HTSlib bindings

finch

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

kun_peng

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

bed2gtf

A fast and memory efficient BED to GTF converter

fqtk

A toolkit for working with FASTQ files

ontolius

A fast and safe crate for working with biomedical ontologies

genome-graph

Representation of genome graphs

wham

weighted histogram analysis method

spiking_neural_networks

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

magpie-bird

eBird Target Bird Scraper

varfish-server-worker

Rust-based worker for varfish-server

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

webgestalt

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

pdbtbx

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

rdkit

High level RDKit functionality for rust

chemical_elements

representing chemical compositions and generating isotopic patterns

slow5

interacting with slow5

wdl-analysis

Analysis of Workflow Description Language (WDL) documents

rumina

High-throughput UMI-aware deduplication of next-generation sequencing data

intspan

Command line tools for IntSpan related bioinformatics operations

miniphy

Create an ordered FASTA TAR file

tskit

rust interface to tskit

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.

coprosize

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

deacon

Fast alignment-free sequence filter

groan_rs

Gromacs Analysis Library for Rust

d4-hts

The htslib binding used by D4

galah

Microbial genome dereplicator

perbase

Fast and correct perbase BAM/CRAM analysis

tgv

Explore genomes in the terminal. Light, blazing fast 🚀, vim-motion.

scidataflow

A command-line tool to manage scientific research project data

minimap2-temp

Bindings to libminimap2

gskits

common kits

phylodm

Efficient calculation of phylogenetic distance matrices

sequenceprofiler

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

exon

A platform for scientific data processing and analysis

rust_abf

reading data from Axon Binary Format (ABF) files

phylotree

deal with phylogenetic trees and distance matrices

fakit

program for fasta file manipulation

kmerutils

Kmer counting, hashing, sequence sketching

fastqc-rs

A fast quality control tool for FASTQ files written in rust

alignoth

creating alignment plots from bam files

bcf_reader

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

crispr_screen

A fast and configurable differential expression analysis tool for CRISPR screens

oxinat

XNAT REST API client

mmft

A minimal fasta toolkit

fqgrep

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

sigalign

A Similarity-Guided Alignment Algorithm

htsget-storage

Storage interfaces and abstractions for htsget-rs

rustynetics

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

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

classeq-cli

A command line interface for the classeq library

genotype_lsp

Genotype language LSP server

packed-seq

Constructing and iterating packed DNA sequences using SIMD

phylo

An extensible Phylogenetics library written in rust

fastlin

an ultra-fast program for MTBC lineage typing

smyl

Artificial Neuronal Network in Rust

dnacomb

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

mehari

Variant effect prediction all in Rust

nail

alignment inference tool

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…

rnapkin

CLI utility for drawing RNA secondary structure

lightmotif-py

PyO3 bindings and Python interface to the lightmotif crate

htsget-test

Common test functions and utilities used by htsget-rs

cribtools

CLI for reading genome track files

eevee

Generalized NeuroEvolution toolkit, based on NEAT

gsetl

etl

kseq

fasta/fastq format parser library

bustools

Interacting with the kallisto/bus format of scRNAseq data

kbo-cli

Command-line interface to the kbo local aligner

check_build

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

compact-genome

Representation of genomes

righor

creates model of Ig/TCR sequences from sequencing data

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

seq-here

A fast tool for bio-sequence file processing

coitrees

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

consalifold

Consensus Secondary Structure Predictor Engaging Structural Alignment-based Error Correction

mzdeisotope

deisotope and charge state deconvolve mass spectra

genomers

Package to download NCBI genome data and metadata

parasail-rs

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

tsalign

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

alevin-fry

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

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…

pombase-gocam

Parser for Gene Ontology Consortium GO-CAM JSON files

varlociraptor

calling of genomic variants using a latent variable model

iirs

Inverted repeats finder

bsalign

Rust bindings for the bsalign C library

fastobo-owl

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

raxtax

k-mer-based non-Bayesian Taxonomic Classifier

librna-sys

Low-level bindings for the ViennaRNA library

wdl

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

ggca

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

wdl-format

Formatting of WDL (Workflow Description Language) documents

genomicsqlite

Genomics Extension for SQLite

dihardts_omicstools

Collection of different omic tools, structs and enums

swc-neuron

CLI utility for interacting with SWC neuronal morphology files

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.

klassify

Classify chimeric reads based on unique kmer contents

atglib

handle transcripts for genomics and transcriptomics

d4-bigwig

The libBigWig binding used by D4

tidyvcf

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

ebiotic

interacting with common bioinformatics web services

light_phylogeny

Methods and functions for phylogeny

tsg-btsg

analyze and manipulate transcript segment graph (TSG)

assembly-theory

Open and Reproducible Computation of Molecular Assembly Indices

easy-rs

reading and processing EEG and accelerometer data from .easy files

codonrs

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

filterx

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

ome_zarr_metadata

OME-Zarr (previously OME-NGFF) metadata

fasta-stats

descriptive statistics on FASTA (biological sequence) data

barcode-count

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

vcfexpress

filtering VCF files using Lua expressions

grumpy

Genetic analysis in Rust

syntesuite

TODO

fxtools

A collection of commandline Fasta/Fastq utility tools

noodles-csi

Coordinate-sorted index (CSI) format reader and writer

ska

Split k-mer analysis

fastq-generator

A fastq generator for generation of synthetic fastq files

microBioRust

Microbiology friendly bioinformatics Rust functions

biodivine-pbn-control

controlling parametrized Boolean networks

jseqio

Reading and writing biological sequences in FASTA or FASTQ format

exon-fastq

FASTQ support for Exon

demes

specification

finalspark-rs

live data recording from MEA devices

give_a_sheet

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

single_rust

Single-cell analysis in Rust

pdbvis

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

crib

CLI for reading and writing genome track files

forgers

VCF manipulation based on FORGe ranking

rosella

Metagenome assembled genome recovery from metagenomes using UMAP and HDBSCAN

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.

hypermash

Genome/Metagenome sketching via HyperMinHash

flowtigs

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

fastq

A parser for fastq

asts

yacrd

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

paraseq

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

dotnetrawfilereader-sys

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

extended-htslib

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

genovo

Determine genes with significantly more mutations than expected by chance

taxonomy

Routines for loading, saving, and manipulating taxonomic trees

scattr

estimating the copy number of large tandem repeats

mikan-rs

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

sirius-bindings

Rust bindings for the SIRIUS metabolomics tool

mm2

minimap2 frontend

phenopackets

Rust bindings for Phenopacket Schema

haptk

Haplotype analysis toolkit

bitnuc

efficient nucleotide sequence manipulation using 2-bit encoding

coverm

Read coverage calculator for metagenomics

nanoq

Minimal but speedy quality control and summaries of nanopore reads

genotype_json_schema

Genotype language JSON Schema crate

bird_tool_utils

Microbial genomics utility functions

interatomic

calculating inter-particle interactions

vcf

VCF Parser

codenano

editing DNA molecular designs

dtw_rs_band_fork

Fork of Dynamic Time Warping Library for Rust

gfatk

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

nafcodec

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

rsvart

A small library for representing genomic variants and regions

fmlrc

FM-index Long Read Corrector - Rust implementation

bioformats-rs

Rust bindings of Bioformats Java library

pdb-handler

functions to handle PDB files

filterx_source

The source library for filterx

rsedlib

rust binding of edlib

lorikeet-genome

Strain resolver and variant caller via local reassembly for metagenomics

ncbitaxonomy

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

tsg

Deep Learning Processing Library for Biological Data

seqalign

Sequence alignment using edit operations

mibig-taxa

NCBI taxdump handling for MIBiG

nthash

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

convert-af

converting alevin-fry output to the AnnData format

tf-binding-rs

Fast transcription factor binding site prediction and FASTA manipulation in Rust

crankshaft

A headless task execution engine that supports local, cloud, and HPC

rna-ss-params

RNA secondary structure parameters

seqkmer

sequence kmer

lightmotif-tfmpvalue

Rust reimplementation of TFMPvalue for the lightmotif crate

benchling

client, generated from the OpenAPI spec

fastax

Make phylogenetic trees and lineages from the NCBI Taxonomy database

viguno

Phenotype/disease for VarFish

lib3dmol

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

genomap

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

groslicer

Slice gro files by processing a stream of lines

genotype_visitor

Genotype language visitor crate

bamrescue

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

knuckles-parse

A tooklkit for parsing PDB records

lib_tsshow

A visualiser for template-switch alignments

kbo

Local alignment search with k-bounded matching statistics

bsxplorer2

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

wdl-doc

Documentation generator for Workflow Description Language (WDL) documents

phenotype-internal

Defines Phenotype trait for Peapod crate

abpoa-rs

Rust bindings for abPOA: Adaptive Banded POA

moleco

generate color swatches for chemical compounds

simd-minimizers

A SIMD-accelerated library to compute random minimizers

ontime

Extract subsets of ONT (Nanopore) reads based on time

bacdive

analyzer for microbial genomics

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…

bvreader

Reader for the BrainVision data format

spikeq

A synthetic FASTQ record generator with pattern spiking

flyteidl

Core Interface Definition for Flyte

clade

phlyo tree, a phylogenetic tree construction software

chainsaw

manipulate newick trees

fastxgz

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

codenano-server

editing DNA molecular designs in a browser

sbwt

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

rsabpoa

abpoa rust binding

nucleob

bioinformatics: nucleobases and amino acids statistics

noodles-vcf

Variant Call Format (VCF) reader and writer

orthanq

quantify haplotypes in an uncertainty-aware manner

frag_gene_scan_rs

gene prediction model for short and error-prone reads

bed-utils

manipulating genomic range objects

gfautil

Command line tools for working with GFA files and related formats

na_seq

DNA and RNA sequence types and functions

tuni

Unify transcripts across different samples

chromsize

just get your chrom sizes

bio-streams

Streaming bioinformatics data types

psylink

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

centraldogma

client for Rust

openslide-sys

Low-level bindings to the openslide library

biodiff-align

Sequence alignment bindings for biodiff

exon-bigwig

Subcrate of the exon crate for working with BigWig files

finch_cli

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

ecdna-lib

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

seqdupes

Compress sequence duplicates

freesasa-sys

Rust raw FFI bindings for the freesasa C library

d4tools

The CLI utils for D4 file format

fire-fasta

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

phenotypes

Common types and traits for modeling clinical information

simd-sketch

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

msbwt2

multi-string BWT query library

bio-read

Bionic reading in terminal

chemcore

A cheminformatics toolkit

webgestalt_lib

computing enrichment for different analytes using ORA or GSEA

blobtk

Core utilities for BlobToolKit

seqcol_rs

implement seqcol in rust

elias_fano_rust

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

sumi

analysis for small RNA libraries with UMIs

consprob

Quick Probability Inference Engine on RNA Structural Alignment

smafa

Read aligner for small pre-aligned sequences

hyper-gen

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

seal

Needleman-Wunsch & Smith-Waterman sequence alignment

metaprofile

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

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

distance_aa

A backend for the distAAnce web application

jam-rs

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

diploid-contam-estimator

Estimating contamination level in diploid DNA seuqencing libraries

lightdock

Macromolecular docking software based on the GSO algorithm

bindashtree

MinHash based phylogenomics via neighbor joining

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.

mni2mz3

Brain imaging surface mesh file format converter

mpileup

Pile up multiple bam files site by site

fpa_lr

fpa filter long read mapping information to save disk space

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

grass-runtime

Runtime library for GRASS

fasta-cleaner

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

fastx

reads Fasta and FastQ files with little overhead

gchemol-gut

Selected utilities for Rust development

ipac

Rust CLI to Install Igor Repositories

thermorawfilereader

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

nohuman

Remove human reads from a sequencing run

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.

minimap2-sys

Bindings to libminimap2

rust-ena

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

crankshaft-engine

The core engine that comprises Crankshaft

crussmap

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

bindash

One Permutation Hashing, Optimal Densification, Genomics

oxbow

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

drug-extraction-core

A core library for extracting drugs from text records

obofoundry

Structures to deserialize OBO Foundry listings into

chemical-formula

Chemical formula parser that can handle wt% and nested structure

guide-counter

Fast and accurate guide counting for CRISPR screens

rustbam

Rust-powered BAM depth extraction with Python bindings

sketchy-rs

Rust command line client for Sketchy

genie-sys

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

seed_chain

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

tsverify

Compare alignments produced by tsalign

gfastats

GFA statistics

winsfs-cli

Site frequency spectrum estimation based on window expectation-maximisation algorithm

bamsalvage

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

genominicus

plot gene trees

vtracker

For tracking the relationship between group membership changes across versions

libprosic

calling of genomic variants using a latent variable model

entrez-rs

Rust wrapper for the Entrez API

bustools_cli

Rust reimplementation of bustools for scRNAseq processing

bio-io

My utilities for reading and writing bioinformatics file formats

grafen

Create graphene and other substrates for use in molecular dynamics simulations

nucleobases

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

rustfastq

bare metal fastq parsing

biostats

A bioinformatics library

gfa-reader

Reading gfa format v1

pattern_partition_prediction

Reading and querying k-mer pattern partition information

omics

Foundations for omics analysis using Rust

fasta

Tools for FASTA reading, writing and indexing

podders

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

maf2bed

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

biofile

reading bioinformatics related files

filterx_info

The builtin function documentation library for filterx

secondary_rewriter

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

fqcat

rapidly merging FASTQ files. Never use cat again!

fasta-filter

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

recmap

reading and working with recombination maps in Rust

pyanndata

Rust APIs

fusta

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

sequence_domain

A DNA/RNA sequence domain

mmap-bitvec

working with bit-vectors backed by memory-mapped files

fasta_windows

Make quick statistics in windows from a fasta file

fastleng

read length statistics tool

gia

set theoretic operations of genomic intervals

biodiff-wfa2-sys

Rust bindings for the WFA2 library

nwbview

Neurodata Without Borders viewer

edlib_rs

interface to the C++ edlib library

bioform

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

optimigation

tools for evolutionary computation, participate GA

noodles-cram

CRAM format reader and writer

prole

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

omics-variation

Foundational representations of variation in the Rust omics ecosystem

census2csv

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

gfa

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

chem-parse

A parser for simple chemical forumulas

nucleociph

encoding phrases into nucleotide characters, and vice versa

debruijn

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

genotype_json_converter

Genotype language JSON tree converter crate

exon-fasta

reading and writing FASTA files with Exon

feos

framework for equations of state and classical density functional theory

tsgen

A random genome generator that generates template switches

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

gtokenizers

tokenizing genomic data with an emphasis on region set data

read-structure

parsing and working with read structure descriptions

slow5lib-sys

Low-level bindings to the slow5lib C library

nii-rs

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

rust-spoa

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

kinesin

re-exports crate (WIP)

vcf_add_ids

Add IDs to VCF records

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.