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Achievement: QuickdrawAchievement: Arctic Code Vault ContributorAchievement: Pull Sharkx2

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4 stars written in Java
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broadinstitute / picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Java 1,061 382 Updated Mar 24, 2026

broadgsa / gatk

Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository

Java 299 223 Updated Aug 22, 2018

samtools / htsjdk

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

Java 297 242 Updated Apr 2, 2026

RealTimeGenomics / rtg-core

RTG Core: Software for alignment and analysis of next-gen sequencing data.

Java 49 11 Updated May 27, 2025