-
needletail
FASTX parsing and k-mer methods
-
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.
-
rust-htslib
HTSlib bindings and a high level Rust API for reading and writing BAM files
-
seq_io
Fast FASTA, FASTQ and FASTX parsing
-
bqtools
A command-line tool for interacting with BINSEQ file formats
-
minimap2
Bindings to libminimap2
-
atg
Convert transcripts between different file formats
-
fqkit
cross-platform program for fastq file manipulation
-
noodles
Bioinformatics I/O libraries
-
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
-
xsra
A performant and storage-efficient CLI tool to extract sequences from an SRA archive with support for FASTA, FASTQ, and BINSEQ outputs
-
rust-bio-tools
A set of fast and robust command line utilities for bioinformatics tasks based on Rust-Bio
-
bio-seq
Bit packed and well-typed biological sequences
-
simpleaf
framework to make using alevin-fry even simpler
-
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…
-
rustyms
handle proteomic mass spectrometry data and match peptides to spectra
-
bigtools
associated tools for reading and writing bigwigs and bigbeds
-
align-cli
A command line interface for easily aligning sequences
-
proseg
Probabilistic cell segmentation for in situ spatial transcriptomics
-
lightmotif
A lightweight platform-accelerated library for biological motif scanning using position weight matrices
-
alignoth
creating alignment plots from bam files
-
rasusa
Randomly subsample reads or alignments
-
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
-
plascad
PlasCAD
-
verify-same-kmer-content
Verify that an SPSS has the same kmer content as a set of unitigs
-
kractor
Extract reads from a FASTQ file based on taxonomic classification via Kraken2
-
rust-lapper
A fast and easy interval overlap library
-
grepq
quickly filter fastq files
-
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
-
wdl
Lexing, parsing, validation, linting, documentation, analysis, and execution for Workflow Description Language (WDL) documents
-
sgcount
A fast and flexible sgRNA counter
-
gb-io
parsing, writing and manipulating Genbank sequence files
-
fastobo
Faultless AST for Open Biomedical Ontologies
-
varfish-server-worker
Rust-based worker for varfish-server
-
fasten
A set of scripts to run basic analysis on fastq files
-
haddock-restraints
Generate restraints to be used in HADDOCK
-
htsget-http
handling HTTP in htsget-rs
-
oarfish
A fast, accurate and versatile tool for long-read transcript quantification
-
sourmash
tools for comparing biological sequences with k-mer sketches
-
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
-
lrge
Genome size estimation from long read overlaps
-
sigalign
A Similarity-Guided Alignment Algorithm
-
genotype_cli
Genotype language CLI
-
nwr
nwris a command line tool for newick and taxonomy -
ontolius
A fast and safe crate for working with biomedical ontologies
-
hgvs
Port of biocommons/hgvs to Rust
-
hts-sys
HTSlib bindings
-
zoe
A nightly library for viral genomics
-
intspan
Command line tools for IntSpan related bioinformatics operations
-
termal-msa
A viewer of multiple sequence alignments, with a text-based user interface
-
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
-
tes
working with the Task Execution Service (TES) specification
-
deepbiop-cli
CLI tool for Processing Biological Data
-
perestroika
genetic algorithms
-
fqtk
A toolkit for working with FASTQ files
-
bed2gtf
A fast and memory efficient BED to GTF converter
-
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
-
mehari
Variant effect prediction all in Rust
-
cardio-rs
computing heart rate variability (HRV) metrics from ECG and PPG data
-
chemical_elements
representing chemical compositions and generating isotopic patterns
-
pdbtbx
open/edit/save (crystallographic) Protein Data Bank (PDB) and mmCIF files
-
rumina
High-throughput UMI-aware deduplication of next-generation sequencing data
-
tgv
Explore genomes in the terminal. Light, blazing fast 🚀, vim-motion.
-
light_phylogeny
Methods and functions for phylogeny
-
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.
-
placecare
A toolkit to quickly search for cis-acting regulatory elements using the PLACE database
-
groan_rs
Gromacs Analysis Library for Rust
-
deacon
Fast alignment-free sequence filter
-
proteogenomics
protein genomics analyzers
-
exon
A platform for scientific data processing and analysis
-
coprosize
coprolite research (paleontology and archaeology): estimate the producer's body mass based on coprolite diameter by the use of regression models
-
galah
Microbial genome dereplicator
-
simd-sketch
A SIMD-accelerated library to compute a b-bit bottom-h sketch
-
refman
A command-line manager for bespoke reference datasets used in bioinformatic analyses
-
scidataflow
A command-line tool to manage scientific research project data
-
mzdeisotope
deisotope and charge state deconvolve mass spectra
-
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
-
minimap2-temp
Bindings to libminimap2
-
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
-
fastlin
an ultra-fast program for MTBC lineage typing
-
lightmotif-py
PyO3 bindings and Python interface to the lightmotif crate
-
dnacomb
Count the occurances of structured sequence reads and compare to an expected library
-
mmft
A minimal fasta toolkit
-
fqgrep
Search a pair of fastq files for reads that match a given ref or alt sequence
-
longcallR
SNP calling and haplotype phasing with long RNA-seq reads
-
phylotree
deal with phylogenetic trees and distance matrices
-
smyl
Artificial Neuronal Network in Rust
-
rustynetics
A high-performance genomics libary specialized in handling BAM and BigWig files
-
phylo
An extensible Phylogenetics library written in rust
-
efficient_pca
Principal component computation using SVD and covariance matrix trick
-
ska
Split k-mer analysis
-
rnapkin
CLI utility for drawing RNA secondary structure
-
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…
-
htsget-actix
A webserver instance of htsget-rs using actix-web, which serves data according to the htsget protocol
-
hypermash
Genome/Metagenome sketching via HyperMinHash
-
parasail-rs
Rust bindings and wrapper for parasail, a SIMD C library for pairwise sequence alignment
-
classeq-cli
A command line interface for the classeq library
-
crispr_screen
A fast and configurable differential expression analysis tool for CRISPR screens
-
eevee
Generalized NeuroEvolution toolkit, based on NEAT
-
crankshaft
A headless task execution engine that supports local, cloud, and HPC
-
bsxplorer2
A high-performance library for bisulfite sequencing data analysis and DNA methylation research
-
kbo-cli
Command-line interface to the kbo local aligner
-
perbase
Fast and correct perbase BAM/CRAM analysis
-
genotype_lsp
Genotype language LSP server
-
bustools
Interacting with the kallisto/bus format of scRNAseq data
-
kseq
fasta/fastq format parser library
-
righor
creates model of Ig/TCR sequences from sequencing data
-
genomers
Package to download NCBI genome data and metadata
-
filterx
A command line tool to filter data by using python-like syntax
-
bsalign
Rust bindings for the bsalign C library
-
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
-
varlociraptor
calling of genomic variants using a latent variable model
-
consalifold
Consensus Secondary Structure Predictor Engaging Structural Alignment-based Error Correction
-
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
-
alevin-fry
A suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data
-
ebiotic
interacting with common bioinformatics web services
-
fastobo-owl
OWL language mapping for ontologies in the OBO flat file format 1.4
-
pombase-gocam
Parser for Gene Ontology Consortium GO-CAM JSON files
-
nthash-rs
Pure‑Rust port of ntHash
-
gskits
common kits
-
extended-htslib
extended HTSlib bindings and a high level Rust API for reading and writing BAM files
-
librna-sys
Low-level bindings for the ViennaRNA library
-
compact-genome
Representation of genomes
-
mm2
minimap2 frontend
-
exon-sdf
Exon SDF
-
fasta-stats
descriptive statistics on FASTA (biological sequence) data
-
paraseq
A minimal-copy parser for FASTA and FASTQ files built for paired parallel processing
-
genominicus
plot gene trees
-
gfatk
command line tool for manipulating small to medium sized GFA files, and specifically for output from the genome assembler MBG
-
fastx
reads Fasta and FastQ files with little overhead
-
fastq-generator
A fastq generator for generation of synthetic fastq files
-
barcode-count
NGS barcode counter for DEL, CRISPR-seq, and Barcode-seq
-
microBioRust
Microbiology friendly bioinformatics Rust functions
-
raxtax
k-mer-based non-Bayesian Taxonomic Classifier
-
sequenceprofiler
sequence similarity based on identity kmers and all sequence profiling under one rust crate
-
scattr
estimating the copy number of large tandem repeats
-
atglib
handle transcripts for genomics and transcriptomics
-
biodivine-pbn-control
controlling parametrized Boolean networks
-
coverm
Read coverage calculator for metagenomics
-
ome_zarr_metadata
OME-Zarr (previously OME-NGFF) metadata
-
seq-here
A fast tool for bio-sequence file processing
-
finalspark-rs
live data recording from MEA devices
-
vcf
VCF Parser
-
wdl-cli
Facilities for building command-line tools using the
wdlcrates -
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.
-
yacrd
Using all-against-all read mapping, yacrd performs: computation of pile-up coverage for each read and detection of chimeras
-
pdbvis
A 3D protein structure viewer that loads and visualizes proteins from the Protein Data Bank (PDB)
-
taxonomy
Routines for loading, saving, and manipulating taxonomic trees
-
packed-seq
Constructing and iterating packed DNA sequences using SIMD
-
genotype_parser
Genotype language parser crate
-
mikan-rs
A medical image kit for segmentation metrics evaluation, native Rust support, and Python bindings for cross-language performance
-
eVaiutilities
variant analyzer for human genomics
-
fastq
A parser for fastq
-
blobtk
Core utilities for BlobToolKit
-
klassify
Classify chimeric reads based on unique kmer contents
-
chromsize
just get your chrom sizes
-
forgers
VCF manipulation based on FORGe ranking
-
give_a_sheet
Toolkit for generating input samplesheets for a variety of nf-core pipelines
-
tsg-cli
analyze and manipulate transcript segment graph (TSG)
-
numpress-rs
A pure rust implementation of ms-numpress, a fast, minimally lossy compression algorithm for mass spectrometry data
-
bitnuc
efficient nucleotide sequence manipulation using 2-bit encoding
-
bindash
One Permutation Hashing, Optimal Densification, Genomics
-
convert-af
converting alevin-fry output to the AnnData format
-
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.
-
nafcodec
Rust coder/decoder for Nucleotide Archive Format (NAF) files
-
interatomic
calculating inter-particle interactions
-
fasta-cleaner
Transform fasta files by upper-casing all sequence characters and removing non-ACGT sequence characters
-
abpoa-rs
Rust bindings for abPOA: Adaptive Banded POA
-
fxtools
A collection of commandline Fasta/Fastq utility tools
-
lorikeet-genome
Strain resolver and variant caller via local reassembly for metagenomics
-
hts
Rust binding for htslib
-
bioformats-rs
Rust bindings of Bioformats Java library
-
fmlrc
FM-index Long Read Corrector - Rust implementation
-
nucleob
bioinformatics: nucleobases and amino acids statistics
-
lightmotif-tfmpvalue
Rust reimplementation of TFMPvalue for the lightmotif crate
-
phenopackets
Rust bindings for Phenopacket Schema
-
ncbitaxonomy
Read NCBI Taxonomy Database from files and work with NCBI Taxonomy DB
-
pdb-handler
functions to handle PDB files
-
noodles-vcf
Variant Call Format (VCF) reader and writer
-
kbo
Local alignment search with k-bounded matching statistics
-
podders
Write uncompressed Pod5 files in native rust. No FFI! PODDDDERS
-
rsvart
A small library for representing genomic variants and regions
-
minimap2-sys
Bindings to libminimap2
-
grumpy
Genetic analysis in Rust
-
nthash
rolling hash function for hashing all possible k-mers in a DNA sequence
-
benchling
client, generated from the OpenAPI spec
-
na_seq
DNA and RNA sequence types and functions
-
orthanq
quantify haplotypes in an uncertainty-aware manner
-
virust-locator
generating sequence locators for HIV/SIV sequences, resembling the functionality of the LANL HIV-Locator tool
-
seal
Needleman-Wunsch & Smith-Waterman sequence alignment
-
lib3dmol
written in rust to read, manipulate, select atoms in protein structure files
-
phenotype-internal
Defines
Phenotypetrait forPeapodcrate -
rna-ss-params
RNA secondary structure parameters
-
genomap
A small library for storing generic genomic data indexed by a chromosome
-
spikeq
A synthetic FASTQ record generator with pattern spiking
-
flyteidl
Core Interface Definition for Flyte
-
ontime
Extract subsets of ONT (Nanopore) reads based on time
-
exon-bigwig
Subcrate of the
exoncrate for working with BigWig files -
bascet
preprocess single-cell data, handling barcode detection, trimming, QC, and managing the execution of custom tools for each cell
-
seqkmer
sequence kmer
-
codonrs
Calculate relative synonymous codon usage for coding DNA sequences in a fasta file
-
bvreader
Reader for the BrainVision data format
-
fastxgz
A fasta/fastq parser for both compressed and not compressed files
-
gfautil
Command line tools for working with GFA files and related formats
-
bio-streams
Streaming bioinformatics data types
-
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…
-
frag_gene_scan_rs
gene prediction model for short and error-prone reads
-
tsg
Deep Learning Processing Library for Biological Data
-
bindashtree
MinHash based phylogenomics via neighbor joining
-
rsabpoa
abpoa rust binding
-
jam-rs
Just another (genomic) minhash (Jam) implementation in Rust
-
slow5lib-sys
Low-level bindings to the slow5lib C library
-
finch_cli
min-wise independent permutation locality sensitive hashing ('MinHashing') for genomic data and command-line utility for manipulation
-
psylink
GUI for PsyLink neural interface for receiving/graphing biosignals and predicting user's intentions
-
bed-utils
manipulating genomic range objects
-
fpa_lr
fpa filter long read mapping information to save disk space
-
filterx_source
The source library for filterx
-
nohuman
Remove human reads from a sequencing run
-
fastax
Make phylogenetic trees and lineages from the NCBI Taxonomy database
-
debruijn
Tools for DNA sequences: efficient k-mer manipulation, De Bruijn graph construction and compaction and handling of DNA strings
-
bsxplorer-ci
A high-performance tool for bisulfite sequencing data analysis and DNA methylation research
-
elias_fano_rust
An optimized implementation of Sebastiano Vigna's Elis-Fano quasi succint datastructure
-
seqdupes
Compress sequence duplicates
-
lightdock
Macromolecular docking software based on the GSO algorithm
-
spdkit
Structure Predication Development Kit
-
bio-read
Bionic reading in terminal
-
distance_aa
A backend for the distAAnce web application
-
sumi
analysis for small RNA libraries with UMIs
-
genotype_visitor
Genotype language visitor crate
-
freesasa-sys
Rust raw FFI bindings for the freesasa C library
-
sketchy-rs
Rust command line client for Sketchy
-
biodiff-align
Sequence alignment bindings for biodiff
-
mni2mz3
Brain imaging surface mesh file format converter
-
mutexpect
functions for determining potential point mutations in a genetic sequence and their statisical probability
-
crussmap
faster tool to convert genome coordinates between difference reference assemblies. Support file formats: [BED,…]. This project reconstructs the CrossMap…
-
bustools_cli
Rust reimplementation of bustools for scRNAseq processing
-
noodles-csi
Coordinate-sorted index (CSI) format reader and writer
-
bamrescue
check Binary Sequence Alignment / Map (BAM) files for corruption and repair them
-
seqcol_rs
implement seqcol in rust
-
ngs
Command line tool for processing next-generation sequencing data
-
simd-minimizers
A SIMD-accelerated library to compute random minimizers
-
fusta
leverages the FUSE interface to transparently manipulate multiFASTA files as independent files
-
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…
-
census-proteomics
working with proteomics data quantified by the Census algorithm
-
xch-ceb
XCH - Chemical Equation Balancer
-
guide-counter
Fast and accurate guide counting for CRISPR screens
-
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
-
consprob
Quick Probability Inference Engine on RNA Structural Alignment
-
sketchlib
Genome and amino-acid sketching
-
chainfile
working with genomics chain files
-
obofoundry
Structures to deserialize OBO Foundry listings into
-
gfastats
GFA statistics
-
drug-extraction-core
A core library for extracting drugs from text records
-
grafen
Create graphene and other substrates for use in molecular dynamics simulations
-
nucleobases
low-level brick crate for managing nucleobases as data in code
-
fire-fasta
Ultra-fast, lazy, zero-copy Multi-FASTA parser
-
mmap-bitvec
working with bit-vectors backed by memory-mapped files
-
dabuild
Access genome build metadata
-
obographs-dev
Load Obographs data files
-
fasta
Tools for FASTA reading, writing and indexing
-
deepbiop-utils
Deep Learning Preprocessing Library for Biological Data
-
rustfastq
bare metal fastq parsing
-
genie-sys
binding for
Genie(A Open Source MPEG-G Codec) -
mzdeisotoper
Deisotoping and charge state deconvolution of mass spectrometry files
-
fasta_windows
Make quick statistics in windows from a fasta file
-
noodles-cram
CRAM format reader and writer
-
nwbview
Neurodata Without Borders viewer
-
optimigation
tools for evolutionary computation, participate GA
-
prole
collection of re-usable methods in Rust. Feel free to use them for your own work.
-
recmap
reading and working with recombination maps in Rust
-
uniprot
Rust data structures and parser for the Uniprot database(s)
-
read-structure
parsing and working with read structure descriptions
-
diced
reimplementation of the MinCED algorithm for identifying CRISPRs in full or assembled genomes
-
bio-jtools
A suite of bioinformatics tools for interacting with high throughput sequencing (HTS) data
-
gfa
working with graphs in the GFA (Graphical Fragment Assembly) format
-
bioform
Tools for sniffing, parsing, and manipulating common biological file formats
-
census2csv
Convert TMT multiplexed proteomics data in the Census format to CSV files
-
protein-translate
Translate nucleotide sequence to protein
-
genotype
An abstraction layer between genotype and phenotype, with in-place mutation
-
gfacut
Cutting out parts of the genome
-
deepbiop
Deep Learning Processing Library for Biological Data
-
entrez-rs
Rust wrapper for the Entrez API
-
strif
identify interruptions in short tandem repeats across the genome
-
seqpls
My sequences please - a paired fastq grepper with regex support
-
ggetrs-enrichr
ggetrs submodule for querying ENRICHR
-
rust-parallelfastx
Parallel iteration of FASTA/FASTQ files, for when sequence order doesn't matter but speed does
-
gdrs
GenomicDistributions package from bioconductor
-
sigalign-utils
utils for core
-
lorikeet-rs
Strain resolver for metagenomics
-
chemical-formula
Chemical formula parser that can handle wt% and nested structure
-
rust-spoa
wraps the C++ SPOA library for generating DNA and protein consensus sequences
-
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
-
nii-rs
reading/writing NIfTI files, with SimpleITK/Nibabel-like APIs, native Rust support, and Python bindings for cross-language performance
-
fastleng
read length statistics tool
-
cytos
A collection of frequently used Bioinformatics scripts/tasks written in Rust
-
xdrfile
Wrapper around the gromacs libxdrfile library. Can be used to read and write gromacs trajectories in xtc and trr format.
-
genotype_json_schema
Genotype language JSON Schema crate
-
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。
-
chembasics
Things for chemistry
-
omnitigs
Omnitig-related algorithms
-
xdf
Read XDF Files
-
fqcat
rapidly merging FASTQ files. Never use cat again!
-
cgt_bacpop
Label core and rare genes in pangenome dataa
-
spoa
wrapper around the spoa C++ SIMD partial order alignment library
-
bacdive
analyzer for microbial genomics
-
exon-cram
Exon CRAM
-
genome
package used to generate DNA used for GAN generator
-
egp
Enzyme Genetic Programming library
-
nu_plugin_bio
Parse and manipulate common bioinformatic formats in nushell
-
proteinogenic
Chemical structure generation for protein sequences as SMILES string
-
phenotypes
Common types and traits for modeling clinical information
-
to-trans
A high-performance transcriptome builder from fasta + GTF/GFF
-
tsg-btsg
analyze and manipulate transcript segment graph (TSG)
-
classeq-watcher
watcher for the Classeq project
-
rumi
PCR Deduplication via directional adjacency
-
microBioRust-seqmetrics
Microbiology friendly bioinformatics Rust functions
-
ross
A set of scripts to run basic analysis on fastq files
-
barkit
— a cross-platform and ultrafast toolkit for barcodes manipulation in FASTQ files
-
rustbam
Rust-powered BAM depth extraction with Python bindings
-
psdm
Compute a pairwise SNP distance matrix from one or two alignment(s)
-
sfasta
Better FASTA sequence compression and querying
-
lib_xch
xch-ceb's official lib
-
libradicl
support library for alevin-fry
-
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.
-
noodles-gff
Generic Feature Format (GFF) reader and writer
-
jean_blosum
BLOSUM feature for jean
-
fg-stitch-lib
Stitch aligner implementation and supporting utilities
-
viguno
Phenotype/disease for VarFish
-
biotest
Generate random test data for bioinformatics
-
aa-regex
macros to build regular expression matching protein sequences
-
vcf_add_ids
Add IDs to VCF records
-
ehxacto
Find exact tandem repeat coordinates from approximate regions identified by ExpansionHunter denovo
-
liblrge
Genome size estimation from long read overlaps
-
noodles-fasta
FASTA format reader and writer
-
seq_io_parallel
A map-reduce style parallel extension to seq_io
-
ffforf
fasta/q/x file format parser. Well fuzzed.
-
pilercr-parser
A parser for the output of the PILER-CR CRISPR array annotation tool
-
exon-io
IO utilities for Exon
-
libwfa2
Bindings to the C implementation of WFA2-lib
-
gsearch
genome classification, probminhash hnsw, genome search
-
clstr
parse and write .clstr files from 'CD-HIT', as well as a small binary with simple functionality
-
consprob-trained
Trainable Probability Inference Engine on RNA Structural Alignment
-
essential
Types for elements, ions and isotopes, the essential and basic units of the matter
-
rust-seq2kminmers
Construction and iteration of k-min-mers from a DNA sequence
-
fasta_split
Split a fasta file into several fasta files
-
filterx_engine
The engine library for filterx
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bamsalvage
Rust version of bamsalvage, retrieving sequences from a corrupted BAM file as much as possible
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gffkit
program for gff3 file manipulation
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chiral-common
Common Stuff of Chiral: An All-in-One Data Processing Tool
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granges
command line tool for genomic range operations
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rosalind-cli
CLI for
rosalindcrate -
gia
set theoretic operations of genomic intervals
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prot_translate
Translate nucleotide sequence to protein
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genotype_project
Genotype language project crate
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exon-benchmarks
Executable benchmarks for exon
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mzdeisotope-map
deisotope and charge state deconvolve mass spectra
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biogarden
A collection of basic bioinformatics algorithms
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handlegraph
in variation graphs
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alpaca
caller for genomic variants (single nucleotide and small indels) from next-generation sequencing data that uses a novel algebraic approach to incorporate sample based filtering into the calling…
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GetPDB
Download Protein files from rcsb.org
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sigalign-core
A core crate for sigalign
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mudskipper
Convert genomic alignments to transcriptomic BAM/RAD files
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libsfasta
Better FASTA sequence compression and querying
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libparasail-sys
Unsafe Rust bindings for the parasail C library
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consalign
RNA Structural Aligner Based on Transfer-learning and Thermodynamic Ensemble Model
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diced-py
PyO3 bindings and Python interface to the diced crate
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modern-arecibo
Generate images of the Arecibo message with a user-provided population and genome size
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multi-seq-align
Manipulate multiple sequence alignments (DNA/protein)
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drprg
Drug resistance prediction with reference graphs
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saboten
biedged graphs, cactus graphs and trees, and an algorithm for finding ultrabubbles in variation graphs
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bsalign_sys
Rust bindings for the bsalign C library
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abpoa-sys
Automatically generated FFI definitions for abPOA
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classeq-api
API for Classeq
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genotype_json_converter
Genotype language JSON tree converter crate
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binseq
A high efficiency binary format for sequencing data
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ambigviz
Identify and plot ambiguous nucleotide bases at given positions from a BAM file
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filterx_info
The builtin function documentation library for filterx
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piscem-infer
A flexible tool to perform target quantification from bulk-sequencing data
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protein
Working with protein structures
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jean
Computational biology utility library for Rust featuring sequence alignment, genome annotation, and I/O of biological files
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ncbi_dl
download ncbi genome file
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sce
importing and managing various single-cell matrices
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nucgen
generating random nucleotide sequences
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fxread
A barebones fastx reader for rust
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chiral-apps
Applications available on chiral
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lightmotif-io
Parser implementations of several formats for the lightmotif crate
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mzsvg
draw mass spectra
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nafcodec-py
PyO3 bindings and Python interface to the nafcodec crate
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minced-parser
A parser for the output of the MinCED CRISPR array annotation tool
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bam-builder
easily building BAMs for testing
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sdust
symmetric DUST algorithm, with optional CLI
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noodles-tabix
Tabix (TBI) format reader and writer