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amplicon-nf

Amplicon genome assembly for ARTIC style primer schemes using Nextflow.

https://github.com/artic-network/amplicon-nf

Science Score: 57.0%

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Last synced: 6 months ago · JSON representation ·

Repository

Amplicon genome assembly for ARTIC style primer schemes using Nextflow.

Basic Info
  • Host: GitHub
  • Owner: artic-network
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Homepage: https://artic.network/
  • Size: 11.7 MB
Statistics
  • Stars: 5
  • Watchers: 6
  • Forks: 0
  • Open Issues: 3
  • Releases: 5
Created about 2 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

artic-network/amplicon-nf

GitHub Actions CI Status Cite with Zenodo

Nextflow nf-core template version run with conda run with docker run with singularity Launch on Seqera Platform

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:

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:

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

Owner

  • Name: ARTICnetwork
  • Login: artic-network
  • Kind: organization

This is the ARTICnetwork project, a Wellcome Trust funded project to provide a system for real-time genomic epidemiology of virus outbreaks.

Citation (CITATIONS.md) 

# artic-network/amplicon-nf: Citations

- [Fieldbioinformatics](https://github.com/artic-network/fieldbioinformatics)

> Loman et al., https://github.com/artic-network/fieldbioinformatics

## Pipeline tools

- [bcftools](https://github.com/samtools/bcftools/)

> Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics (2011) 27(21) 2987-93.

- [bwa](https://github.com/lh3/bwa)

> Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2

- [clair3](https://github.com/HKU-BAL/Clair3)
  
> Zheng, Z., Li, S., Su, J. et al. Symphonizing pileup and full-alignment for deep learning-based long-read variant calling. Nat Comput Sci 2, 797–803 (2022). https://doi.org/10.1038/s43588-022-00387-x

- [minimap2](https://github.com/lh3/minimap2)

> Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34:3094-3100. doi:10.1093/bioinformatics/bty191  

- [mafft](http://mafft.cbrc.jp/alignment/software/)

> Kazutaka Katoh, Kazuharu Misawa, Kei‐ichi Kuma, Takashi Miyata, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Research, Volume 30, Issue 14, 15 July 2002, Pages 3059–3066, https://doi.org/10.1093/nar/gkf436

- [pandas](https://github.com/pandas-dev/pandas)

> The pandas development team. (2025). pandas-dev/pandas: Pandas (v2.3.0). Zenodo. https://doi.org/10.5281/zenodo.15597513

- [pysam](https://github.com/pysam-developers/pysam)

> Heger et al., https://github.com/pysam-developers/pysam

- [cyvcf2](https://github.com/brentp/cyvcf2)

> Brent S Pedersen, Aaron R Quinlan, cyvcf2: fast, flexible variant analysis with Python, Bioinformatics, Volume 33, Issue 12, June 2017, Pages 1867–1869, https://doi.org/10.1093/bioinformatics/btx057

- [samtools](https://github.com/samtools/samtools)

> Twelve years of SAMtools and BCFtools Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008

- [seqtk](https://github.com/lh3/seqtk)

> Li et al., https://github.com/lh3/seqtk

- [plotly](https://github.com/plotly/plotly.py)

> Plotly Technologies Inc. (2015). Collaborative data science. Montreal, QC: Plotly Technologies Inc. Retrieved from https://plot.ly

- [biopython](https://github.com/biopython/biopython)

> Cock, P.J.A. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3 https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878

- [primalbedtools](https://github.com/ChrisgKent/primalbedtools)

> Kent, C., Smith, A. D., Tyson, J., Stepniak, D., Kinganda-Lusamaki, E., Lee, T., Weaver, M., Sparks, N., Landsdowne, L., Wilkinson, S. A., Brier, T., Colquhoun, R., O’Toole, A. N., Kingebeni, P. M., Goodfellow, I. G., Rambaut, A., Loman, N. J., & Quick, J. (2024). PrimalScheme: open-source community resources for low-cost viral genome sequencing. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.12.20.629611

- [freebayes](https://github.com/freebayes/freebayes)

> Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012

- [Seqkit](https://github.com/shenwei356/seqkit)

> Shen, W., Le, S., Li, Y., & Hu, F. (2016). SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLOS ONE, 11(10), e0163962. https://doi.org/10.1371/journal.pone.0163962

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

## Nextflow

- [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

- [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

GitHub Events

Total
  • Create event: 8
  • Release event: 1
  • Issues event: 11
  • Watch event: 4
  • Delete event: 5
  • Issue comment event: 9
  • Public event: 1
  • Push event: 56
  • Pull request event: 11
Last Year
  • Create event: 8
  • Release event: 1
  • Issues event: 11
  • Watch event: 4
  • Delete event: 5
  • Issue comment event: 9
  • Public event: 1
  • Push event: 56
  • Pull request event: 11

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 8
  • Total pull requests: 7
  • Average time to close issues: 30 days
  • Average time to close pull requests: about 4 hours
  • Total issue authors: 5
  • Total pull request authors: 2
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.57
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 8
  • Pull requests: 7
  • Average time to close issues: 30 days
  • Average time to close pull requests: about 4 hours
  • Issue authors: 5
  • Pull request authors: 2
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.57
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • BioWilko (3)
  • ammaraziz (2)
  • rmcolq (1)
  • ChrisgKent (1)
  • John-Tyson (1)
Pull Request Authors
  • BioWilko (6)
  • rambaut (1)
Top Labels
Issue Labels
enhancement (4) bug (2)
Pull Request Labels

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