Official code repository for GATK versions 4 and up

Java utilities for Bioinformatics

A Java API for high-throughput sequencing data (HTS) formats.

Cloud agnostic genomics analysis, scientific computation and storage platform

ABRA2

HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.

A library for manipulating bioinformatics sequencing formats in Apache Spark

BBTools: Official suite of fast, multithreaded bioinformatics tools for DNA/RNA analysis. BBMap aligner, BBDuk trimmer, BBMerge, and 90+ other tools. Actively maintained by Brian Bushnell.

This is the SeqWare Project's main repo.

A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage

A reference guided assembler of highly variable viral genomes

The mitochondrial workbench

Fonda is a framework which offers scalable and automatic analysis of multiple NGS sequencing data types

MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data; MegaPath-Amplicon: filtering module for metagenomic amplicon data

A Universal Toolkit for Handling Sequence Data from Different Sequencing Platforms

sparkhit - analyzing large scale genomic data on the cloud

MiTools: yet another Next Generation Sequencing (NGS) data processing tool (based on MiLib)

Big Data tool for scalable short-read error correction

A Reliable and Fast Algorithm for Single Individual Haplotyping