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readsimulator

A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.

https://github.com/nf-core/readsimulator

Science Score: 31.0%

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    Found 10 DOI reference(s) in README
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Keywords

nextflow nf-core pipeline workflow
Last synced: 10 months ago · JSON representation ·

Repository

A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.

Basic Info
Statistics
  • Stars: 32
  • Watchers: 177
  • Forks: 8
  • Open Issues: 12
  • Releases: 1
Topics
nextflow nf-core pipeline workflow
Created almost 3 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nf-core/readsimulator

GitHub Actions CI Status GitHub Actions Linting StatusAWS CICite with Zenodo nf-test

Nextflow run with conda run with docker run with singularity Launch on Seqera Platform

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Introduction

nf-core/readsimulator is a pipeline to simulate sequencing reads. The pipeline currently supports simulating amplicon, target capture, metagenome, and wholegenome data. It takes a samplesheet with sample names and seeds for random generation to produce simulated FASTQ files and a samplesheet that contains the paths to the FASTQ files.

nf-core/readsimulator workflow overview

Amplicon simulation steps

  1. Create reference database for amplicon-based sequencing (CRABS)
  2. Simulate amplicon Illumina reads (art_illumina)
  3. Create samplesheet with sample names and paths to simulated read files (header = sample,fastq1,fastq2)
  4. Simulated read QC (FastQC)
  5. Present QC for simulated reads (MultiQC)

Target capture simulation steps

  1. Align probes to genome (Bowtie2)
  2. Get SAM index (SAMtools)
  3. Simulate target capture reads (Illumina (default) or Pacbio) (Japsa capsim)
  4. Create samplesheet with sample names and paths to simulated read files (header = sample,fastq1,fastq2)
  5. Simulated read QC (FastQC)
  6. Present QC for simulated reads (MultiQC)

Metagenome simulation steps

  1. Simulate metagenome Illumina reads (InsilicoSeq Generate)
  2. Create samplesheet with sample names and paths to simulated read files (header = sample,fastq1,fastq2)
  3. Simulated read QC (FastQC)
  4. Present QC for simulated reads (MultiQC)

Wholegenome simulation steps

  1. Simulate wholegenome reads (wgsim)
  2. Create samplesheet with sample names and paths to simulated read files (header = sample,fastq1,fastq2)
  3. Simulated read QC (FastQC)
  4. Present QC for simulated reads (MultiQC)

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,seed sample_1,1 sample_2,4

Each row represents an output sample.

Now, you can run the pipeline using:

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

[!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.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/readsimulator was originally written by Adam Bennett for use at the Minderoo Foundation's OceanOmics project.

We thank the following people for their extensive assistance in the development of this pipeline (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 the Slack #readsimulator channel (you can join with this invite).

Citations

If you use nf-core/readsimulator for your analysis, please cite it using the following doi: 10.5281/zenodo.10622410

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

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.

Owner

  • Name: nf-core
  • Login: nf-core
  • Kind: organization
  • Email: core@nf-co.re

A community effort to collect a curated set of analysis pipelines built using Nextflow.

Citation (CITATIONS.md) 

# nf-core/readsimulator: Citations

## [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.

## Pipeline tools

- [ART](https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm)

  > Weichun Huang, Leping Li, Jason R. Myers, Gabor T. Marth, ART: a next-generation sequencing read simulator, Bioinformatics, Volume 28, Issue 4, February 2012, Pages 593–594, https://doi.org/10.1093/bioinformatics/btr708

- [bedtools](https://pubmed.ncbi.nlm.nih.gov/20110278/)

  > Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842. hhtps://doi.org/10.1093/bioinformatics/btq033

- [Bowtie2](https://www.nature.com/articles/nmeth.1923)

  > Langmead, B., Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357–359 (2012). https://doi.org/10.1038/nmeth.1923

- [CapSim](https://academic.oup.com/bioinformatics/article/34/5/873/4575140)

  > Minh Duc Cao, Devika Ganesamoorthy, Chenxi Zhou, Lachlan J M Coin, Simulating the dynamics of targeted capture sequencing with CapSim, Bioinformatics, Volume 34, Issue 5, March 2018, Pages 873–874, https://doi.org/10.1093/bioinformatics/btx691

- [CRABS](https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13741)

  > Jeunen, G.-J., Dowle, E., Edgecombe, J., von Ammon, U., Gemmell, N. J., & Cross, H. (2022). crabs—A software program to generate curated reference databases for metabarcoding sequencing data. Molecular Ecology Resources, 00, 1– 14. https://doi.org/10.1111/1755-0998.13741

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [InSilicoSeq](https://academic.oup.com/bioinformatics/article/35/3/521/5055123)

  > Gourlé H, Karlsson-Lindsjö O, Hayer J and Bongcam+Rudloff E, Simulating Illumina data with InSilicoSeq. Bioinformatics (2018) doi:10.1093/bioinformatics/bty630

- [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.

- [ncbi-genome-download](https://zenodo.org/records/8192486)

  > DOI: 10.5281/zenodo.8192432

- [Samtools](https://academic.oup.com/gigascience/article/10/2/giab008/6137722?login=false)

  > 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

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

## Reference probe/baitset databases

All reference probe databases are sourced from [ultraconserved](https://www.ultraconserved.org/)

- [Tetrapods; 2,560 baits for 2,386 UCEs; version 1](https://academic.oup.com/sysbio/article/61/5/717/1735316)

  > Brant C. Faircloth, John E. McCormack, Nicholas G. Crawford, Michael G. Harvey, Robb T. Brumfield, Travis C. Glenn, Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales, Systematic Biology, Volume 61, Issue 5, October 2012, Pages 717–726, https://doi.org/10.1093/sysbio/sys004

- [Tetrapods; 5,472 baits for 5,060 UCEs; version 1](https://royalsocietypublishing.org/doi/10.1098/rspb.2014.0823)

  > Sun Keping, Meiklejohn Kelly A., Faircloth Brant C., Glenn Travis C., Braun Edward L. and Kimball Rebecca T., 2014 The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach. Proc. R. Soc. B. 281: 20140823. 20140823. http://doi.org/10.1098/rspb.2014.0823

- [Actinopterygians; 2,001 baits for 500 UCEs; version 1](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065923)

  > Faircloth BC, Sorenson L, Santini F, Alfaro ME (2013) A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs). PLOS ONE 8(6): e65923. https://doi.org/10.1371/journal.pone.0065923

- [Acanthomorphs; 2,628 baits for 1,314 UCEs; version 1](https://royalsocietypublishing.org/doi/10.1098/rspb.2015.1413)

  > McGee Matthew D., Faircloth Brant C., Borstein Samuel R., Zheng Jimmy, Darrin Hulsey C., Wainwright Peter C. and Alfaro Michael E.. 2016 Replicated divergence in cichlid radiations mirrors a major vertebrate innovation. Proc. R. Soc. B. 283: 20151413. 20151413. http://doi.org/10.1098/rspb.2015.1413

- [Arachnida; 14,799 baits for 1,120 UCEs; version 1](https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12621)

  > Starrett, J., Derkarabetian, S., Hedin, M., Bryson Jr. R. W., McCormack. J. E., & Faircloth. B. C. (2016). High phylogenetic utility of an Ultraconserved element probe set designed for Arachnida. Molecular Ecology Resources. 17(4), 812-823. https://doi.org/10.1111/1755-0998.12621

- [Coleoptera; 13,674 baits for 1,172 UCEs; version 1](https://resjournals.onlinelibrary.wiley.com/doi/10.1111/syen.12244)

  > Baca. S. M., Alexander. A., Gustafson. G. T., & Short. A. E. Z. (2017). Ultraconserved elements show utility in phylogenetic inference of Adephaga (Coleoptera) and suggest paraphyly of Hydradephaga. 42(4), 786-795. https://doi.org/10.1111/syen.12244

- [Diptera; 31,328 baits for 2,711 UCEs; version 1](https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.12754)

  > Faircloth. B. C. (2017). Identifying conserved genomic elements and designing universal bait sets to enrich them. Methods in Ecology and Evolution. 8(9), 1103-1112. https://doi.org/10.1111/2041-210X.12754

- [Hemiptera; 40,207 baits for 2,731 UCEs; version 1](https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.12754)

  > Faircloth. B. C. (2017). Identifying conserved genomic elements and designing universal bait sets to enrich them. Methods in Ecology and Evolution. 8(9), 1103-1112. https://doi.org/10.1111/2041-210X.12754

- [Hymenoptera; 2,749 baits for 1,510 UCEs; version 1](https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12328)

  > Faircloth. B. C., Branstetter. M. G., White. N. D., & Brady. S. G. (2014). Target enrichment of ultraconserved elements from anthropods provides a genomic perspective on elationships among Hymenoptera. Molecular Ecology Resources. 15(3), 489-501. https://doi.org/10.1111/1755-0998.12328

- [Hymenoptera; 31,829 baits for 2,590 UCEs; version 2](https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.12742)

  > Branstetter. M. G., Longino. J. T., Ward. P. S., & Faircloth. B. C. (2017). Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera. 8(6), 768-776. https://doi.org/10.1111.2041-210X.12742

- [Anthozoa; 16,306 baits for 720 UCEs and 1,071 exons; version 1](https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12736)

  > Quattrini. A. M., Faircloth. B. C., Duenas. L. F., Bridge. T. C. L., Brugler. M. R., Calixto-Botia. I. F., DeLeo. D. M., Foret. S., Herrera. S., Lee. S. M. Y., Miller. D. J., Prada. C., Radis-Baptista. G., Ramirez-Portilla. C., Sanchez. J. A., Rodriguez. E., & McFadden. C. S. (2017). Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems. Molecular Ecology Resources. 18(2), 281-295. https://doi.org/10.1111/1755-0998.12736

## 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.

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Dependencies

.github/workflows/awsfulltest.yml actions
  • actions/upload-artifact v3 composite
  • seqeralabs/action-tower-launch v2 composite
.github/workflows/awstest.yml actions
  • actions/upload-artifact v3 composite
  • seqeralabs/action-tower-launch v2 composite
.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • actions/checkout v3 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/clean-up.yml actions
  • actions/stale v7 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
.github/workflows/linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
  • mshick/add-pr-comment v1 composite
  • nf-core/setup-nextflow v1 composite
  • psf/black stable composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact v2 composite
  • marocchino/sticky-pull-request-comment v2 composite
modules/nf-core/art/illumina/meta.yml cpan
modules/nf-core/bowtie2/align/meta.yml cpan
modules/nf-core/bowtie2/build/meta.yml cpan
modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/samtools/index/meta.yml cpan
pyproject.toml pypi