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fxtools
A collection of commandline Fasta/Fastq utility tools
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exon
A platform for scientific data processing and analysis
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exon-fasta
reading and writing FASTA files with Exon
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exon-io
IO utilities for Exon
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exon-sam
Exon SAM
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exon-gtf
GTF datasource for Exon
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exon-fcs
Exon FCS
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exon-genbank
Exon GenBank
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exon-cram
Exon CRAM
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exon-bam
Exon BAM
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exon-fastq
FASTQ support for Exon
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exon-bed
Subcrate of the
exon
crate for working with BED files -
exon-bcf
Exon BCF
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noodles
Bioinformatics I/O libraries
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parasail-rs
Rust bindings and wrapper for parasail, a SIMD C library for pairwise sequence alignment
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exon-common
Common utilities for Exon
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exon-mzml
Exon MzML
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righor
creates model of Ig/TCR sequences from sequencing data
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exon-vcf
Exon VCF
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noodles-cram
CRAM format reader and writer
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fqkit
cross-platform program for fastq file manipulation
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lightdock
Macromolecular docking software based on the GSO algorithm
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bedblocks
Split a BED file into blocks
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libparasail-sys
Unsafe Rust bindings for the parasail C library
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prot_translate
Translate nucleotide sequence to protein
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primaldimer_rs
calculating PrimerPrimer interactions
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fakit
program for fasta file manipulation
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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
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rust-bio-tools
A set of fast and robust command line utilities for bioinformatics tasks based on Rust-Bio
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freesasa-sys
Rust raw FFI bindings for the freesasa C library
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atg
Convert transcripts between different file formats
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mehari
Variant effect prediction all in Rust
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noodles-htsget
An htsget client
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noodles-refget
A refget client
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noodles-gff
Generic Feature Format (GFF) reader and writer
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noodles-gtf
Gene Transfer Format (GTF) reader and writer
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gdrs
GenomicDistributions package from bioconductor
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give_a_sheet
Toolkit for generating input samplesheets for a variety of nf-core pipelines
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varlociraptor
calling of genomic variants using a latent variable model
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crispr_screen
A fast and configurable differential expression analysis tool for CRISPR screens
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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.
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sourmash
tools for comparing biological sequences with k-mer sketches
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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
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sprocket
A package manager for the Workflow Description Language files
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ebiotic
interacting with common bioinformatics web services
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ffforf
fasta/q/x file format parser. Well fuzzed.
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minimap2
Bindings to libminimap2
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minimap2-sys
Bindings to libminimap2
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granges
command line tool for genomic range operations
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recmap
reading and working with recombination maps in Rust
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ska
Split k-mer analysis
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seqsizzle
A pager for viewing FASTQ files with fuzzy matching, allowing different adaptors to be colored differently
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slow5lib-sys
Low-level bindings to the slow5lib C library
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alevin-fry
A suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data
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libradicl
support library for alevin-fry
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seqrepo
Port of (read-only) functionality of biocommons/seqrepo to Rust
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alignoth
creating alignment plots from bam files
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genome
package used to generate DNA used for GAN generator
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scidataflow
A command-line tool to manage scientific research project data
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hgvs
Port of biocommons/hgvs to Rust
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oarfish
A fast, accurate and versatile tool for long-read transcript quantification
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simplr
An augmented execution context to simplify long-read transcriptome analysis
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piscem-infer
A flexible tool to perform target quantification from bulk-sequencing data
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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
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bvreader
Reader for the BrainVision data format
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rust-htslib
HTSlib bindings and a high level Rust API for reading and writing BAM files
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fasten
A set of scripts to run basic analysis on fastq files
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light_phylogeny
Methods and functions for phylogeny
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bed-utils
manipulating genomic range objects
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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…
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stats_on_genomes
Calculate 2 simple ratio on the whole genome: GC ratio and repetition ratio
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bustools
Interacting with the kallisto/bus format of scRNAseq data
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align-cli
A command line interface for easily aligning sequences
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genomap
A small library for storing generic genomic data indexed by a chromosome
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sgcount
A fast and flexible sgRNA counter
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ontime
Extract subsets of ONT (Nanopore) reads based on time
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bigtools
associated tools for reading and writing bigwigs and bigbeds
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bed-reader
Read and write the PLINK BED format, simply and efficiently
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bustools_cli
Rust reimplementation of bustools for scRNAseq processing
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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.
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simpleaf
framework to make using alevin-fry even simpler
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nail
alignment inference tool
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libnail
that performs profile Hidden Markov Model (PHMM) biological sequence alignment
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oxbow
Read specialized bioinformatic file formats as data frames in R, Python, and more
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sorensen
Sørensen–Dice coefficient implementation for Rust
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blobtk
Core utilities for BlobToolKit
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cgt_bacpop
Label core and rare genes in pangenome dataa
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alpine-core
ALPINE (Anachronistic Lineage and Persistent INfection Explorer) Core Utilities
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dihardts_omicstools
Collection of different omic tools, structs and enums
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fastx
reads Fasta and FastQ files with little overhead
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coverm
Read coverage calculator for metagenomics
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galah
Microbial genome dereplicator
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bird_tool_utils
Microbial genomics utility functions
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webgestalt
CLI for computing enrichment for different analytes using ORA or GSEA
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haptk
Haplotype analysis toolkit
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podders
Write uncompressed Pod5 files in native rust. No FFI! PODDDDERS
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rosella
Metagenome assembled genome recovery from metagenomes using UMAP and HDBSCAN
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rasusa
Randomly subsample reads to a specified coverage
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fxread
A barebones fastx reader for rust
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htsget-test
Common test functions and utilities used by htsget-rs
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to-trans
A high-performance transcriptome builder from fasta + GTF/GFF
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atglib
handle transcripts for genomics and transcriptomics
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maf2bed
Converts multiple alignment format (MAF) files to a BED format for tabixing. Used with jbrowse-plugin-mafviewer
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nale
that performs profile Hidden Markov Model (PHMM) biological sequence alignment
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wdl
Document lexing, parsing, validation, and linting for Workflow Description Language (WDL) documents
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lightmotif
A lightweight platform-accelerated library for biological motif scanning using position weight matrices
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sigalign
A Similarity-Guided Alignment Algorithm
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nohuman
Remove human reads from a sequencing run
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lightmotif-py
PyO3 bindings and Python interface to the lightmotif crate
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lightmotif-tfmpvalue
Rust reimplementation of TFMPvalue for the lightmotif crate
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lightmotif-transfac
TRANSFAC parser implementation for the lightmotif crate
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sigalign-utils
utils for core
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sigalign-core
A core crate for sigalign
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lightmotif-io
Motif parsers implementation for the lightmotif crate
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sigalign-impl
implementations for core
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kmerutils
Kmer counting, hashing, sequence sketching
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lorikeet-genome
Strain resolver and variant caller via local reassembly for metagenomics
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bio-seq
Bit packed and well-typed biological sequences
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pedigree
Build a pedigree from WGS data
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methylome
Structs and methods for working with methylation data
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chainsaw
manipulate newick trees
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jam-rs
Just another (genomic) minhash (Jam) implementation in Rust
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gia
set theoretic operations of genomic intervals
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prole
collection of re-usable methods in Rust. Feel free to use them for your own work.
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cytos
A collection of frequently used Bioinformatics scripts/tasks written in Rust
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mni2mz3
Brain imaging surface mesh file format converter
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fastxgz
A fasta/fastq parser for both compressed and not compressed files
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readmerger
rapidly merging FASTQ files. Never use cat again!
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wham
weighted histogram analysis method
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verify-same-kmer-content
Verify that an SPSS has the same kmer content as a set of unitigs
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exon-test
Exon test crate
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biocommons-bioutils
(Partial) port of biocommons/bioutils to Rust
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uniprot
Rust data structures and parser for the Uniprot database(s)
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pipspeak
converting PIPSeq files to 10X Genomics compatible FASTQ files
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exon-benchmarks
Executable benchmarks for exon
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gtfjson
convert GTF files to newline-delim JSON
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kmers
k-mer manipulation
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scispeak
converting Sci-RNA-Seq3 files to 10X Genomics compatible FASTQ files
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flowtigs
An algorithm for calculating flowtigs in a De Bruijn graph of DNA reads in metagenomes
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kinesin
re-exports crate (WIP)
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ggetrs
Efficient querying of biological databases from the command line
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kractor
Extract reads from a FASTQ file based on taxonomic classification via Kraken2
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mmap-bitvec
working with bit-vectors backed by memory-mapped files
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krakenxtract
Extract reads from a FASTQ file based on taxonomic classification via Kraken2
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librna-sys
Low-level bindings for the ViennaRNA library
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bedrs
Genomic interval library in rust
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prepare_fasta
Compute hash-based signatures of sequence, and perform pre-processing
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bam-builder
easily building BAMs for testing
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kgst
containing the implementation of a K-Truncated Generalized Suffix Tree using Ukkonen's Algorithm
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phylotree
deal with phylogenetic trees and distance matrices
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splici
generate spliced and unspliced reference transcripts for sequence alignment
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nwr
nwr
is a command line tool for newick and taxonomy -
chainfile
working with genomics chain files
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slow5
interacting with slow5
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pdbtbx
open/edit/save (crystallographic) Protein Data Bank (PDB) and mmCIF files
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sfs-cli
Tools for working with site frequency spectra
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gffkit
program for gff3 file manipulation
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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
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syntesuite
TODO
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omnitigs
Omnitig-related algorithms
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genome-graph
Representation of genome graphs
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compact-genome
Representation of genomes
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fastix
prefix renaming FASTA records
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intspan
Command line tools for IntSpan related bioinformatics operations
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readfish-tools
Tools for analysing adaptive sampling data
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fqtk
A toolkit for working with FASTQ files
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gtftools
A barebones GTF toolkit with fast nom-based IO
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fastlin
an ultra-fast program for MTBC lineage typing
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ncbi
Rust data structures for NCBI APIs
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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
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fffx
fasta/q/x file format parser. Well fuzzed.
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sce
importing and managing various single-cell matrices
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chiral-common
Common Stuff of Chiral: An All-in-One Data Processing Tool
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perbase
Fast and correct perbase BAM/CRAM analysis
-
consprob-trained
Trainable Probability Inference Engine on RNA Structural Alignment
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skc
Shared k-mer content between two genomes
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disambiseq
Create unambiguous one-off mismatch libraries for DNA sequences
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smafa
Read aligner for small pre-aligned sequences
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hts-sys
HTSlib bindings
-
strif
identify interruptions in short tandem repeats across the genome
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tca
A platform for scientific data processing and analysis
-
read-structure
parsing and working with read structure descriptions
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intc
*-INC method to calculate an empirical FDR for non-targeting controls in CRISPR screens
-
rnapkin
CLI utility for drawing RNA secondary structure
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protein_translation
translate &str or String of RNA sequence with nucleotide into a Vec<&str> of their appropriate protein names
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fastobo
Faultless AST for Open Biomedical Ontologies
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gsearch
genome classification, probminhash hnsw, genome search
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fastleng
read length statistics tool
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gfatk
command line tool for manipulating small to medium sized GFA files, and specifically for output from the genome assembler MBG
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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.
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seq_geom_xform
Transform/normalize complex single-cell fragment geometries into simple geometries
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drprg
Drug resistance prediction with reference graphs
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seq_geom_parser
A small crate for parsing library geometry specifications for single-cell sequencing
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needletail
FASTX parsing and k-mer methods
-
ngs
Command line tool for processing next-generation sequencing data
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fastax
Make phylogenetic trees and lineages from the NCBI Taxonomy database
-
nucleic-acids
creating DNA and RNA sequences
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nwbview
Neurodata Without Borders viewer
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seqsample
Randomly sample sequences from a FASTA file
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chiral-apps
Applications available on chiral