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1. broadinstitute/gatk broadinstitute/gatk Public

   Official code repository for GATK versions 4 and up

   Java 2k 625

2. samtools/htsjdk samtools/htsjdk Public

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

   Java 299 242

3. broadinstitute/barclay broadinstitute/barclay Public

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

   Java 12 6

4. broadinstitute/cromshell broadinstitute/cromshell Public

   CLI for interacting with Cromwell servers

   Python 54 15

5. disq-bio/disq disq-bio/disq Public

   A library for manipulating bioinformatics sequencing formats in Apache Spark

   Java 33 12

6. broadinstitute/http-nio broadinstitute/http-nio Public

   Forked from magicDGS/jsr203-http

   HTTP/S FileSystem provider for Java NIO.2

   Java 2 1