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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/gatk-bwamem-jni broadinstitute/gatk-bwamem-jni Public

   JNI code for bwa mem

   Java 3 4

4. broadinstitute/gatk-native-bindings broadinstitute/gatk-native-bindings Public

   GATK Native Bindings Repository

   Java 3 2

5. jopt-simple/jopt-simple jopt-simple/jopt-simple Public

   Java library for parsing command line options

   Java 353 67

6. broadinstitute/barclay broadinstitute/barclay Public

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

   Java 9 6