NBISweden/biovat

Introduction

BioVAT (Biodiversity Variant Analysis Toolkit) is a modular Nextflow pipeline for mapping, variant calling, data filtering and downstream analyses of population-level whole genome resequencing data.

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample,library_id,flowcell_id,lane,platform,fastq_1,fastq_2
SAMPLE_1,1,AEG588A1,2,illumina,/path/to/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/AEG588A1_S1_L002_R2_001.fastq.gz

Each row represents a set of paired-end FASTQ files generated from a specific sample library and run on a specific flowcell lane.

Next, create a parameter file for your run based on the example file assets/nf-params.yml and fill out all relevant parameters.

Now, you can run the pipeline using:

nextflow run NBISweden/biovat \
   -profile <singularity/conda/.../dardel/arrhenius/pelle> \
   -params-file assets/my-run-params.yml

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

BioVAT was originally written by Verena Kutschera, Mahesh Binzer-Panchal, Cormac Kinsella, André Soares, Jason Hill, Lorena Ament, Per Unneberg, and Lucile Soler.

We thank the following people for their extensive assistance in the development of this pipeline:

Filip Thörn
Henrik Lantz
Jacob Höglund
Jesper Boman
José Cerca
Mafalda Ferreira
Niclas Backström

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.