nf-core/exoseq

Name: exoseq

Owner: nf-core

Description: Exome Sequencing analysis pipeline (Work in progress)

Created: 2018-04-18 14:45:49.0

Updated: 2018-05-22 11:38:31.0

Pushed: 2018-05-07 15:57:32.0

Homepage: http://nf-co.re

Size: 2847

Language: Nextflow

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README

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
3. Local installation
4. Amazon Web Services
5. Swedish UPPMAX clusters
6. Swedish cs3e Hebbe cluster
7. Tübingen QBiC clusters
8. Adding your own system
9. Running the pipeline
10. Preparing custom exome capture kits
11. Output and how to interpret the results
12. 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.