Rust Bioinformatics Resources

Warning kerblam run and kerblam package are complete but still untested. Please do use them, but be careful. Always have a backup of your data and cod

bed2gff A Rust BED-to-GFF3 translator. translates chr7 56766360 56805692 ENST00000581852.25 1000 + 56766360 56805692 0,0,200 3 3,135,81, 0,496,39251,

biobear is a Python library designed for reading and searching bioinformatic file formats, using Rust as its backend and producing Arrow Batch Readers

skc skc is a simple tool for finding shared k-mer content between two genomes. Installation Prebuilt binary curl -sSL skc.mbh.sh | sh # or with wget w

oxbow Read specialized bioinformatic file formats as data frames in R, Python, and more. File formats create a lot of friction for computational biolo

🎼 🧬 lightmotif A lightweight platform-accelerated library for biological motif scanning using position weight matrices. 🗺️ Overview Motif scanning

🐍 ⛓️ 🧬 Pyskani PyO3 bindings and Python interface to skani, a method for fast fast genomic identity calculation using sparse chaining. 🗺️ Overview

xgt xgt is a Rust tool that enables efficient querying and parsing of the GTDB database. xgt consists of a collection of commands mirroring the GTDB A

DNArchery 🧬 A free and open-source cross-platform DNA Sequencing/Visualization Software for bioinformatics research. A toolkit for instantly performi

best Bam Error Stats Tool (best): analysis of error types in aligned reads. best is used to assess the quality of reads after aligning them to a refer

Lomanai Usage lomanai --species 'Mus musculus' --species 'Homo sapiens' # Mammalia # ++Rodentia # | \-Mus musculus # \+Primates # \-Homo sapien

Nushell bio A bioinformatics plugin for nushell. The aim initially is to create a bunch of parsers for all of the common bioinformatics file formats a

vircov Minimal virus genome coverage assessment for metagenomic diagnostics Overview v0.5.0 Purpose Implementation Installation Usage Tests Concept Cl

proteinogenic Chemical structure generation for protein sequences as SMILES string. 🔌 Usage This crate builds on top of purr, a crate providing primi

pubchem.rs Rust data structures and client for the PubChem REST API. 🔌 Usage 💊 Compound Create a Compound to query the PubChem API for a single comp

guide-counter A better, faster way to count guides in CRISPR screens. Overview guide-counter is a tool for processing FASTQ files from CRISPR screen e

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

Compute a pairwise SNP distance matrix from one or two alignment(s) Table of Contents Motivation Install cargo conda Precompiled binaries homebrew Con

Rustyread is a drop in replacement of badread simulate. Rustyread is very heavily inspired by badread, it reuses the same error and quality model file. But Rustyreads is multi-threaded and benefits from other optimizations.