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Introduction

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

The implementation of nf-core/artic is an international collaboration between numerous contributors and developers. We appreciated the need to have a portable, reproducible and scalable pipeline for the analysis of COVID-19 sequencing samples and so the Avengers Assembled! Please come and join us and add yourself to the contributor list :)

This pipeline is a re-implementation of the amazing work already carried out by contributors to the ARTIC Network's field bioinformatics pipeline and their associated bioinformatics protocol. Matt Bull's Nextflow implementation was also used for some much needed inspiration.

The plan is to fully containerise and support both pre-demultiplexed Nanopore and Illumina data in the same workflow.

If you need to demultiplex Nanopore data beforehand you can use the Guppy implementation in the nf-core/nanoseq pipeline (NOTE: GPUs are also supported) The parameters you provide will depend on the protocol you used to sequence the samples (see usage docs). An example command:

nextflow run nf-core/nanoseq \
    --input samplesheet.csv \
    --protocol DNA \
    --input_path ./fast5/ \
    --flowcell FLO-MIN106 \
    --kit SQK-LSK109 \
    --barcode_kit SQK-PBK004 \
    -profile <docker/singularity/institute>

Quick Start

i. Install nextflow

ii. Install either Docker or Singularity for full pipeline reproducibility

iii. Download the pipeline and test it on a minimal dataset with a single command

nextflow run nf-core/artic -profile test,<docker/singularity/institute>

Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.

iv. Start running your own analysis!

nextflow run nf-core/artic -profile <docker/singularity/conda/institute> --input samplesheet.csv

See usage docs for all of the available options when running the pipeline.

Documentation

The nf-core/artic pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Pipeline configuration
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting

Credits

Name Affiliation
Alexander Peltzer Boehringer Ingelheim, Germany
Gisela Gabernet QBIC, University of Tubingen, Germany
Harshil Patel The Francis Crick Institute, UK
Matt Bull Public Health Wales, UK
Maxime Garcia SciLifeLab, Sweden
Michael Heuer UC Berkeley, USA
Nick Loman University of Birmingham, UK
Olga Botvinnik Chan Zuckerberg Biohub, USA
Phil Ewels SciLifeLab, Sweden
Thanh Le Viet Quadram Institute, UK
Will Rowe University of Birmingham, UK

Listed in alphabetical order

Contributions and Support

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

For further information or help, don't hesitate to get in touch on Slack (you can join with this invite).

Citation

You can cite the nf-core publication as follows:

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.
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