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1. broadinstitute/gatk broadinstitute/gatk Public

   Official code repository for GATK versions 4 and up

   Java 1.7k 594

2. samtools/htsjdk samtools/htsjdk Public

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

   Java 285 244

3. broadinstitute/barclay broadinstitute/barclay Public

   Command line argument parser and online documentation generation utilities for java command line programs.

   Java 9 6

4. broadinstitute/picard broadinstitute/picard Public

   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 984 369

5. samtools/hts-specs samtools/hts-specs Public

   Specifications of SAM/BAM and related high-throughput sequencing file formats

   TeX 658 172

6. bramtools bramtools Public

   Playground for genomics using Rust.

   Rust