An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Python and C++ code for reading and writing genomics data.

The next version of bwa-mem

A high-performance, Pythonic language for bioinformatics

A fast and sensitive gapped read aligner

Versatile open-source tool for microbiome analysis

Ultra-fast and memory-efficient (meta-)genome assembler

Signal-level algorithms for MinION data

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

Haplotype VCF comparison tools

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

Structural variant and indel caller for mapped sequencing data

RAxML Next Generation: faster, easier-to-use and more flexible

Toolset for SV simulation, comparison and filtering

Strelka2 germline and somatic small variant caller

🔬 Assemble large genomes using short reads

Bayesian haplotype-based mutation calling

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.