This pipeline has been moved to the new nf-core GitHub organisation. You can now
find it here:
This repository will be archived to maintain the release version for future reproducibility, to allow reruns.
If you have any questions, please get in touch: [email protected]
// Phil Ewels, 2018-04-18
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
The NGI-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) and has been adapted by Alex Peltzer (@apeltzer) and Marie Gauder (@mgauder) to our needs at QBiC, Tübingen, Germany.
In addition, we would like to recognise:
- Developers at SciLifeLab in Stockholm, Sweden
- Developers at National Genomics Infrastructure for their help, supports and suggestions
- UPPMAX team
- Nextflow team
- BWA team
- GATK team
- PICARD team
- SnpEff team
NGI-ExoSeq is now used by a number of core sequencing and bioinformatics facilities. Some of these are listed below. If you use this pipeline too, please let us know in an issue and we will add you to the list.
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National Genomics Infrastructure (NGI), Sweden | https://ngisweden.scilifelab.se/ |
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Quantitative Biology Center (QBiC), Germany | https://portal.qbic.uni-tuebingen.de/portal/ |
