A collection of genomics software tools written in Rust

• alignoth : Creating alignment plots from bam files
• bamrescue : Utility to check Binary Sequence Alignment / Map (BAM) files for corruption and repair them
• best : Bam Error Stats Tool (best): analysis of error types in aligned reads
• modkit : A bioinformatics tool for working with modified bases
• mapAD : An aDNA aware short-read mapper
• perbase : Per-base per-nucleotide depth analysis
• rustybam : bioinformatics toolkit in rust

• csview : 📠 Pretty and fast csv viewer for cli with cjk/emoji support
• csvlens : csvlens is a command line CSV file viewer. It is like less but made for CSV.
• madato : Markdown Cmd Line, Rust and JS library for Excel to Markdown Tables
• qsv : Blazing-fast Data-Wrangling toolkit
• rsv : A command-line tool written in Rust for analyzing CSV, TXT, and Excel files.
• tabiew : A lightweight TUI app to view and query CSV files
• tv : 📺(tv) Tidy Viewer is a cross-platform CLI csv pretty printer that uses column styling to maximize viewer enjoyment.
• xan : The CSV magician
• xsv : A fast CSV command line toolkit written in Rust.  
• xtab : CSV command line utilities

• biotools : Command line bioinformatics functions
• darwin : Create (rapid) neighbor-joining tree from sequences using mash distance
• fakit : fakit: a simple program for fasta file manipulation
• filterx : process any file in tabular format. Fasta/fastq/GTF/GFF/VCF/SAM/BED
• fq : Command line utility for manipulating Illumina-generated FASTQ files.
• gsearch : Approximate nearest neighbour search for microbial genomes based on hash metric
• Hyper-Gen : HyGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors
• kanpig : Kmer Analysis of Pileups for Genotyping
• kfc : KFC (K-mer Fast Counter) is a fast and space-efficient k-mer counter based on hyper-k-mers.
• ngs : Command line utility for working with next-generation sequencing files.
• nail : Nail is an Alignment Inference tooL
• palindrome-finder : A bioinformatics tool written in Rust to find palindromic sequences in DNA
• poasta : Fast and exact gap-affine partial order alignment
• psdm : Compute a pairwise SNP distance matrix from one or two alignment(s)
• rust-bio-tools : A set of command line utilities based on Rust-Bio.
• sigalign : A Similarity-Guided Alignment Algorithm
• ska : Split k-mer analysis – version 2
• skc : Shared k-mer content between two genomes
• sketchy : Genomic neighbor typing of bacterial pathogens using MinHash 🐀
• tidk : Identify and find telomeres, or telomeric repeats in a genome.
• transanno : accurate LiftOver tool for new genome assemblies
• xgt : Efficient and fast querying and parsing of GTDB's data

• deacon : Fast (host) DNA sequence filtering
• fasten : 👷 Fasten toolkit, for streaming operations on fastq files
• faster : A (very) fast program for getting statistics about a fastq file, the way I need them, written in Rust
• fqgrep : Grep for FASTQ files
• fqkit : 🦀 Fqkit: A simple and cross-platform program for fastq file manipulation  
• fqtk : Fast FASTQ sample demultiplexing in Rust.
• grepq: quickly filter fastq files by matching sequences to a set of regex patterns
• guide-counter : A better, faster way to count guides in CRISPR screens.
• K2Rmini : K2Rmini (or K-mer to Reads mini) is a tool to filter the reads contained in a FASTA/Q file based on a set of k-mers of interest.
• kractor : Rapidly extract reads from a FASTQ file based on taxonomic classification via Kraken2.
• rasusa : Randomly subsample sequencing reads
• SeqSizzle : SeqSizzle is a pager for viewing FASTQ files with fuzzy matching, allowing different adaptors to be colored differently.
• sabreur : fast, reliable and handy demultiplexing tool for fastx files

• atlas : Enables storing, querying, transforming, and visualizing of multidimensional count data.
• bigtools : A high-performance BigWig and BigBed library in Rust
• biotest : Generate random test data for bioinformatics
• bqtools : A command line utilty for working with BINSEQ files
• cigzip : A tool for compression and decompression of alignment CIGAR strings using tracepoints.
• d4tools : The D4 Quantitative Data Format
• gfa2bin : Convert various graph-related data to PLINK file. In addition, we offer multiple commands for filtering or modifying the generated PLINK files.
• gia : gia: Genomic Interval Arithmetic
• granges : A Rust library and command line tool for working with genomic ranges and their data.
• intspan : Command line tools for IntSpan related bioinformatics operations
• nuc2bit : A rust crate that provides methods for rapidly encoding and decoding nucleotides in 2-bit representation.
• recmap : A command line tool and Rust library for working with recombination maps.
• transanno : accurate LiftOver tool for new genome assemblies
• thirdkind : Drawing reconciled phylogenetic trees allowing 1, 2 or 3 reconcillation levels
• xsra : An efficient CLI to extract sequences from the SRA

• atg : A Rust library and CLI tool to handle genomic transcripts
• gffkit : a simple program for gff3 file manipulation

• Autocycler : A tool for generating consensus long-read assemblies for bacterial genomes
• chopper : Rust implementation of NanoFilt+NanoLyse, both originally written in Python. This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file.
• DeepChopper : Language models identify chimeric artificial reads in NanoPore direct-RNA sequencing data.
• fpa : Filter of Pairwise Alignement
• herro : HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).
• HiPhase : Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads
• isONclust3 : De novo clustering of long transcript reads into genes
• longshot : diploid SNV caller for error-prone reads
• lrge : Genome size estimation from long read overlaps
• myloasm : A new high-resolution long-read metagenome assembler for even noisy reads
• Polypolish : a short-read polishing tool for long-read assemblies
• nextpolish2 : Repeat-aware polishing genomes assembled using HiFi long reads
• nanoq : Minimal but speedy quality control for nanopore reads in Rust 🐻
• smrest : Tumour-only somatic mutation calling using long reads
• trgt : Tandem repeat genotyping and visualization from PacBio HiFi data
• yacrd : Yet Another Chimeric Read Detector

• coverm : Read coverage calculator for metagenomics
• galah : More scalable dereplication for metagenome assembled genomes
• hyperex : Hypervariable region primer-based extractor for 16S rRNA and other SSU/LSU sequences.
• kun_peng : Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all
• kmertools : kmer based feature extraction tool for bioinformatics, metagenomics, AI/ML and more
• kmerutils : Kmer generating, counting hashing and related
• Lorikeet : Strain resolver for metagenomics
• nohuman : Remove human reads from a sequencing run
• rosella : Metagenomic Binning Algorithm
• skani : Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
• sourmash : Quickly search, compare, and analyze genomic and metagenomic data sets.
• sylph : ultrafast genome querying and taxonomic profiling for metagenomic samples by abundance-corrected minhash.
• vircov : Viral genome coverage evaluation for metagenomic diagnostics 🩸

• impg : implicit pangenome graph
• panacus : Panacus is a tool for computing statistics for GFA-formatted pangenome graphs

• nextclade : Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
• nwr : nwr is a command line tool for working with NCBI taxonomy, Newick files and assembly reports
• unicore : Universal and efficient core gene phylogeny with Foldseek and ProstT5
• segul : An ultrafast and memory efficient tool for phylogenomics

• align-cli : A CLI for pairwise alignment of sequences, using both normal and mass based alignment.
• daedalus : Protein and molecule viewer
• folddisco : Fast indexing and search of discontinuous motifs in protein structures
• foldmason : Foldmason builds multiple alignments of large structure sets.
• sage : Proteomics search & quantification so fast that it feels like magic

• oarfish : long read RNA-seq quantification
• rnapkin : drawing RNA secondary structure with style; instantly
• R2Dtool : R2Dtool is a set of genomics utilities for handling, integrating, and viualising isoform-mapped RNA feature data.
• squab : Alignment-based gene expression quantification

• adview : Adata Viewer: Head/Less/Shape h5ad file in terminal
• alevin-fry : 🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
• cellranger : 10x Genomics Single Cell Analysis
• precellar : Single-cell genomics preprocessing package
• proseg : Probabilistic cell segmentation for in situ spatial transcriptomics
• SnapATAC2 : Single-cell epigenomics analysis tools

• ssubmit : Submit slurm sbatch jobs without the need to create a script
• wdl : Rust crates for working with Workflow Description Language (WDL) documents.

• echtvar : using all the bits for echt rapid variant annotation and filtering
• gvcf_norm : gVCF allele normalizer
• mehari: VEP-like tool for sequence ontology and HGVS annotation of VCF files
• vcf2parquet : Convert vcf in parquet
• vcfexpress : expressions on VCFs
• vcf-reformatter : 🧬 High-performance VCF file parser and reformatter with VEP annotation support. Converts complex VCF files to analyzable TSV format with intelligent transcript handling.

• plascad : Design software for plasmid (vector) and primer creation and validation. Edit plasmids, perform PCR-based cloning, digest and ligate DNA fragments, and display details about expressed proteins. Integrates with online resources like NCBI and PDB.

• biobear : Work with bioinformatic files using Arrow, Polars, and/or DuckDB
• binseq : A high efficiency binary format for sequencing data
• exon : Exon is an OLAP query engine specifically for biology and life science applications.
• ggetrs : Efficient querying of biological databases
• htsget-rs : A server implementation of the htsget protocol for bioinformatics in Rust
• ibu : a rust library for high throughput binary encoding of genomic sequences
• scidataflow: Command line scientific data management tool
• sufr : Parallel Construction of Suffix Arrays in Rust