Liftoff.bio
Liftoff.bio illustration — cat genomics
Open sourceGenomics & Sequencing

GATK

Broad Institute toolkit for variant discovery

WebsiteSource codeDocumentationContainerPublication

GATK is the Broad Institute's toolkit for variant discovery in high-throughput sequencing data. Its Best Practices workflows for germline SNPs/indels and somatic mutations are an industry standard.

Highlights

  • HaplotypeCaller and Mutect2 for germline and somatic calling.
  • Scales with Spark and runs well under WDL/Cromwell and Nextflow.
  • Distributed as a container for reproducible pipelines.

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Liftoff.bio illustration — cat genomics
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Liftoff.bio illustration — cat workflows
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Cromwell & WDL

Workflow engine for the Workflow Description Language

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Liftoff.bio illustration — cat workflows
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Workflow Orchestration

nf-core

A community library of curated Nextflow pipelines

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