nfcore/exoseq repository overview

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.