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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 1,057 383 Updated Mar 24, 2026

pcingola / SnpEff

Java 303 86 Updated Mar 9, 2026

mkirsche / Jasmine

Jasmine: SV Merging Across Samples

Java 245 21 Updated Dec 20, 2024

nextflow-io / language-server

The Nextflow language server

Java 28 5 Updated Mar 27, 2026