SciLifeLab/NGI-ExoSeq

Name: NGI-ExoSeq

Owner: Science For Life Laboratory

Description: (WIP) Nextflow Exome Sequencing Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure. https://ngisweden.scilifelab.se/

Forked from: senthil10/NGI-ExoSeq

Created: 2017-08-08 10:27:56.0

Updated: 2017-10-31 15:54:25.0

Pushed: 2018-01-15 21:25:17.0

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Size: 1810

Language: Groovy

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README

Introduction

NGI-ExoSeq is a bioinformatics package that performs best-practice analysis pipeline for Exome Sequencing data at the National Genomics Infastructure at SciLifeLab Stockholm, Sweden.

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 NGI-ExoSeq pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation and configuration
2. Running the pipeline
3. Output and how to interpret the results

Credits

These scripts were written for use at the National Genomics Infrastructure at SciLifeLab in Stockholm, Sweden. The pipeline was developed by Senthilkumar Panneerselvam (@senthil10) with a little help from Phil Ewels (@ewels).

In addition, we would like to recognise:

• Developers at National Genomics Infrastructure for their help, supports and suggestions
• UPPMAX team
• Nextflow team
• BWA team
• GATK team
• PICARD team
• SnpEff team

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