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5 stars written in Java
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broadinstitute / gatk

Official code repository for GATK versions 4 and up

Java 1,894 622 Updated Dec 18, 2025

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 1,037 382 Updated Nov 13, 2025

s-andrews / FastQC

A quality control analysis tool for high throughput sequencing data

Java 558 105 Updated Dec 15, 2025

jernst98 / ChromHMM

Java 91 19 Updated Jul 6, 2025

enasequence / ena-ftp-downloader

Java based tools for bulk downloading read/analysis files from ENA via FTP or Aspera.

Java 43 7 Updated Jun 13, 2025