Official code repository for GATK versions 4 and up
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Jul 17, 2026 - Java
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Bioinformatics
Bioinformatics is an interdisciplinary field that intersects with biology, computer science, mathematics and statistics. It concerns itself with the development and use of methods and software tools for collecting and analyzing biological data.
Here are 299 public repositories matching this topic...
📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.
java bioinformatics genomics pdb parser-library protein-data-bank protein-structure protein-sequences sequence-alignment protein-modification structure-alignment structural-bioinformatics
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Jun 30, 2026 - Java
The Chemistry Development Kit
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Jul 7, 2026 - Java
Java utilities for Bioinformatics
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Jul 17, 2026 - Java
A powerful open source data warehouse system
python java api open-source clojure opensource bioinformatics genomics genetics clojurescript biology perl postgresql lgplv3 tomcat data-visualization data-warehouse data-visualisation webservices tomcat8
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Jun 24, 2026 - Java
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
bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases
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Dec 19, 2025 - Java
Pegasus Workflow Management System - Automate, recover, and debug scientific computations.
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Jul 20, 2026 - Java
The Pharmacogenomic Clinical Annotation Tool
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Jul 19, 2026 - Java
Precision genomics for everyone, everywhere. Powered by private AI.
cli open-source machine-learning privacy bioinformatics genomics computational-biology artificial-intelligence fasta biotechnology precision-medicine dna-sequencing on-device regulatory-elements dna-analysis
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Jul 19, 2026 - Java
SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)
java science bioinformatics cheminformatics molecular-structures sirius metabolomics mass-spectrometry ms-data denovo molecular-formulas ms-spectra structure-elucidation fragmentation-trees csi-fingerid fingerid isotope-pattern mass-spectra
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Jul 17, 2026 - Java
Global Biotic Interactions provides access to existing species interaction datasets
bioinformatics parasites biology diet ecology biodiversity diseases eol etl-framework food-webs ecoinformatics globi species-interactions pollinators
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Jul 18, 2026 - Java
Apache cTAKES is a Natural Language Processing (NLP) platform for clinical text.
nlp emr bioinformatics medicine ai ml clinical healthcare named-entity-recognition uima ehr umls ctakes temporal-information
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May 18, 2026 - Java
An app store for scientific workflows, tools, notebooks, and services
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Jul 16, 2026 - Java
MOLGENIS - for scientific data: management, exploration, integration and analysis.
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Mar 4, 2026 - Java
Bio4j abstract model and general entry point to the project
java bioinformatics database graph proteins protein gene-ontology java-8 graph-database ncbi-taxonomy graph-databases property-graph graph-data uniprot bio4j graph-queries graph-schema titan bio4j-titan uniref
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Dec 16, 2016 - Java
OWLTools
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Jul 7, 2026 - Java
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.
java bioinformatics quality-control genomics assembly ngs sequencing sam alignment fastq adapter-trimming error-correction bbmap tadpole bbduk clumpify bbnorm callvariants bbcms bbmerge
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Jul 17, 2026 - Java
Annotation of VCF variants with functional impact and from databases (executable+library)
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Jul 13, 2026 - Java
PDV: an integrative proteomics data viewer
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Jul 6, 2026 - Java
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