nfcore/ExoSeq is a bioinformatics analysis pipeline that performs best-practice analysis pipeline for Exome Sequencing data.

The pipeline is built based on GATK best practices using Nextflow, a bioinformatics workflow tool. The main steps done by pipeline are the following (more information about the processes can be found here).

  • Alignment
  • Marking Duplicates
  • Recalibration
  • Realignment
  • Variant Calling
  • Variant Filtration
  • Variant Evaluation
  • Variant Annotation


The nfcore/ExoSeq pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Pipeline installation and configuration instructions
  2. Pipeline configuration
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting


The pipeline was initally developed by Senthilkumar Panneerselvam (@senthil10) with a little help from Phil Ewels (@ewels) at the National Genomics Infrastructure, part of SciLifeLab in Stockholm and has been extended by Alex Peltzer (@apeltzer), Marie Gauder (@mgauder) from QBIC Tuebingen/Germany as well as Marc Hoeppner (@marchoeppner) from IKMB Kiel/Germany.

Many thanks also to others who have helped out along the way too, including @pditommaso, @colindaven.