README.md

This is still work in practice, but will hopefully soon be a stable version that will then be published in a release version.

Introduction

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

Documentation

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

1. Pipeline installation and configuration instructions
2. Pipeline configuration
   • Local installation
   • Amazon Web Services
   • Swedish UPPMAX clusters
   • Swedish cs3e Hebbe cluster
   • Tübingen QBiC clusters
   • Adding your own system
3. Running the pipeline
   • Preparing custom exome capture kits
4. Output and how to interpret the results
5. Troubleshooting

Credits

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.