Official code repository for GATK versions 4 and up

📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Java utilities for Bioinformatics

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

MISO: An open-source LIMS for NGS sequencing centres

A powerful open source data warehouse system

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

A Tool to Annotate and Prioritize Exome Variants

Democratizing ML-powered DNA analysis through efficient on-device computation and interpretive tools.

AQUAS TF and histone ChIP-seq pipeline

VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications

Various utilities regarding Levenshtein transducers. (Java)

CGView is a Java package for generating high-quality, zoomable maps of circular genomes.

GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using declarative query language, in a parallel execution engine.

EzAAI - High Throughput Prokaryotic AAI Calculator

forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research

Efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing

A library for manipulating bioinformatics sequencing formats in Apache Spark

UFCG: Universal Fungal Core Genes

A Java Desktop application with a graphical user interface for the discovery of colinear syntenic blocks across thousands microbial genomes