This is still work in practice, but will hopefully soon be a stable version that will then be published in a release version.
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:
- Pipeline installation and configuration instructions
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
- 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.