Introduction

artic-network/amplicon-nf is a bioinformatics pipeline that takes sequencing reads generated from ARTIC-style viral amplicon sequencing schemes, assembles them into consensus sequences, and runs some basic quality control on the outputs.

Acknowledgements

This pipeline has been created as part of the ARTIC network project funded by the Wellcome Trust (collaborator award – 313694/Z/24/Z and discretionary award – 206298/Z/17/Z) and is distributed as open source and open access. All non-code files are made available under a Creative Commons CC-BY licence unless otherwise specified. Please acknowledge or cite this repository or associated publications if used in derived work so we can provide our funders with evidence of impact in the field.

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,barcode,platform,scheme_name,custom_scheme_path,custom_scheme_name,fastq_directory,fastq_1,fastq_2
nanopore_amplicon_data,,nanopore,artic-inrb-mpox/2500/v1.0.0,,,/path/to/fastq/files/Barcode01/,,,
illumina_amplicon_data,,illumina,,/path/to/custom_scheme/,some_scheme_name,,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz

The scheme_name field refers to a scheme as a primalscheme labs identifier e.g. artic-inrb-mpox/2500/v1.0.0 or artic-sars-cov-2/400/v5.4.2.

Each row represents a fastq file (single-end) or a pair of fastq files (paired end), the pipeline will run the Illumina and ONT workflows in parallel, it is important to note that the ONT and Illumina workflows have different input requirements. ONT requires only fastq_directory which is intended to be a directory as created by Dorado / minKNOW during basecalling. Below there is an example layout of a fastq_pass directory, each row of the samplesheet in this case would point to a single barcode directory.

Note

There are more detailed pipeline / Nextflow usage instructions (including samplesheet construction and custom primer schemes), there are available in: docs/usage.md.

Now, you can run the pipeline using:

nextflow run artic-network/amplicon-nf \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR> \
   --store_dir <STOREDIR> 

The pipeline is configured with a set of default parameters which should suit most use cases but a full list of available configurable parameters is available in docs/parameters.md.

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.

Problems and Solutions

If you run into problems running this pipeline there is a list of known problems and their solutions available in docs/problems.md. If the issue you encounter is not listed there please consider making an issue!

Credits

artic-network/amplicon-nf was originally written by Sam Wilkinson (@BioWilko).

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

• James A. Fellows Yates (@jfy133), Áine O'Toole (@aineniamh), Rachel Colquhoun (@rmcolq), Chris G. Kent (@ChrisgKent), Bede Constantinides (@bede) and Andrew Rambaut (@rambaut) for the extremely useful testing and feedback.
• Jared Simpson (@jts) for originally writing the Illumina Freebayes consensus generation workflow the Illumina workflow is based on.

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.