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
- 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
- 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
- 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
- rust-bio-tools : A set of command line utilities based on Rust-Bio.
- 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.
- tidk : Identify and find telomeres, or telomeric repeats in a genome.
- xgt : Efficient and fast querying and parsing of GTDB's data
- 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.
- rasusa : Randomly subsample sequencing reads
- bigtools : A high-performance BigWig and BigBed library in Rust
- 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
- recmap : A command line tool and Rust library for working with recombination maps.
- thirdkind : Drawing reconciled phylogenetic trees allowing 1, 2 or 3 reconcillation levels
- 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.
- 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
- longshot : diploid SNV caller for error-prone reads
- lrge : Genome size estimation from long read overlaps
- 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
- coverm : Read coverage calculator for metagenomics
- 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
- nohuman : Remove human reads from a sequencing run
- 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
- 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.
- 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
- 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
- echtvar : using all the bits for echt rapid variant annotation and filtering
- mehari: VEP-like tool for sequence ontology and HGVS annotation of VCF files
- vcf2parquet : Convert vcf in parquet
- vcfexpress : expressions on VCFs
- biobear : Work with bioinformatic files using Arrow, Polars, and/or DuckDB
- 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