The Fast Cross-Platform Package Manager

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

A library for reading text files over multiple cores.

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

SPAdes Genome Assembler

A fast and sensitive gapped read aligner

Versatile open-source tool for microbiome analysis

A single molecule sequence assembler for genomes large and small.

hybrid assembly pipeline for bacterial genomes

SeqAn's official repository.

Graph-based alignment (Hierarchical Graph FM index)

A fast multi-threaded k-mer counter

C++ API & command-line toolkit for working with BAM data

Fast genome and metagenome distance estimation using MinHash

C Python, made faster.

Bayesian haplotype-based mutation calling

Fast and frugal disk based k-mer counter

Classifier for metagenomic sequences

samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.

Kraken taxonomic sequence classification system

A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

Population-scale genotyping using pangenome graphs

Scalable gVCF merging and joint variant calling for population sequencing projects

Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)

A robust and fast clustering method for amplicon-based studies

Efficient clustering of next generation sequences

Genome inference from a population reference graph

LAMBDA – the Local Aligner for Massive Biological DatA