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seqaudit-nf

https://github.com/doh-hnh0303/seqaudit-nf

Science Score: 57.0%

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  • Host: GitHub
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  • License: mit
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Created 9 months ago · Last pushed 8 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

nf-core/seqaudit

GitHub Actions CI Status GitHub Actions Linting StatusCite with Zenodo nf-test

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

Introduction

SeqAudit is a bioinformatics pipeline that simulates ONT, PacBio, and Illumina sequencing data'

Create a set of fastq files from an input reference genome fasta. You can provide the number of sample sets that you wish to create for each technology type (Illumina fastq will be created as paired end reads) and provide the reference genome as a path, RefSeq, or Genbank ID.

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:

Example samplesheet.csv

sample_id,genome_source,genome_id,ont_reads,pacbio_reads,illumina_reads sample1,refseq,GCF_000001405.39,10000,5000,1000000 sample2,genbank,GCA_000005825.2,5000,8000,500000 sample3,local,/path/to/genome.fasta,0,10000,2000000 ecoli,refseq,GCF_000005825.2,15000,12000,800000 Each row represents the creation of X number of a fastq files (single-end) or pairs of fastq files (paired end) for a specific sequencing technology

Now, you can run the basic pipeline using:

```bash

Simulate ONT, PacBio, and Illumina reads

nextflow run main.nf \ --input samplesheet.csv \ --outdir results \ -profile docker ```

You can also provide more parameters for use with specific sequencing technologies

[!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

SeqAudit was originally written by Holly Halstead.

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: Holly Halstead
  • Login: DOH-HNH0303
  • Kind: user
  • Company: Washington State Department of Health

Bioinformatician (Epidemiologist III)

Citation (CITATIONS.md) 

# SeqAudit: Citations
If you use the SeqAudit pipeline, please cite the following tools and resources:
Core Pipeline Framework

### [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.

## Sequencing Data Simulation Tools

### [PBSIM3](https://doi.org/10.1093) (ONT and PacBio simulation)

    Ono, Y., Asai, K., & Hamada, M. (2021). PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores. Bioinformatics, 37(5), 589-595. https://doi.org/10.1093/bioinformatics/btaa835
    Ono, Y., Hamada, M., & Asai, K. (2013). PBSIM: PacBio reads simulator--toward accurate genome assembly. Bioinformatics, 29(1), 119-121. https://doi.org/10.1093/bioinformatics/bts649

### [NanoSim](https://doi.org/10.1093/gigascience/gix010) (ONT simulation alternative)

    Yang, C., Chu, J., Warren, R. L., & Birol, I. (2017). NanoSim: nanopore sequence read simulator based on statistical characterization. GigaScience, 6(4), gix010. https://doi.org/10.1093/gigascience/gix010

### [ART](https://doi.org/10.1093/bioinformatics/btr708) (Illumina simulation)

    Huang, W., Li, L., Myers, J. R., & Marth, G. T. (2012). ART: a next-generation sequencing read simulator. Bioinformatics, 28(4), 593-594. https://doi.org/10.1093/bioinformatics/btr708


## Data Retrieval and Processing

### [NCBI Entrez Direct](https://www.ncbi.nlm.nih.gov/books/NBK179288/)

    Kans, J. (2013). Entrez Direct: E-utilities on the Unix Command Line. In Entrez Programming Utilities Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US). Available from: https://www.ncbi.nlm.nih.gov/books/NBK179288/

### [MultiQC](https://doi.org/10.1093/bioinformatics/btw354) (Quality Control Reporting)

    Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047-3048. https://doi.org/10.1093/bioinformatics/btw354

## Container and Environment Management

### Docker

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

### [Singularity](https://doi.org/10.1371/journal.pone.0177459)

    Kurtzer, G. M., Sochat, V., & Bauer, M. W. (2017). Singularity: Scientific containers for mobility of compute. PLoS ONE, 12(5), e0177459. https://doi.org/10.1371/journal.pone.0177459

### [Conda](https://docs.anaconda.com/)

    Anaconda Software Distribution. (2020). Anaconda Documentation. Anaconda Inc. Retrieved from https://docs.anaconda.com/

### [Bioconda](https://doi.org/10.1038/s41592-018-0046-7)

    Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., ... & Köster, J. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475-476. https://doi.org/10.1038/s41592-018-0046-7

## Wave Container Provisioning

### [Wave](https://seqera.io/wave/)

    Seqera Labs. (2023). Wave: Container provisioning service for Nextflow pipelines. Retrieved from https://seqera.io/wave/

### Additional Resources
## Reference Databases

### [NCBI RefSeq](https://doi.org/10.1093/nar/gkv1189)

    O'Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., ... & Pruitt, K. D. (2016). Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Research, 44(D1), D733-D745. https://doi.org/10.1093/nar/gkv1189

### [NCBI GenBank](https://doi.org/10.1093/nar/gkw1070)

    Benson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2017). GenBank. Nucleic Acids Research, 45(D1), D37-D42. https://doi.org/10.1093/nar/gkw1070

Citation Format

When citing the SeqAudit pipeline in your publications, please use the following format:
We used the SeqAudit pipeline (version X.X.X) for simulating [ONT/PacBio/Illumina] sequencing data.
The pipeline utilizes [PBSIM3/NanoSim] for long-read simulation and ART for Illumina read simulation,
implemented in Nextflow (Di Tommaso et al., 2017).
Software Versions

The specific versions of software used in your analysis can be found in the MultiQC report generated by the pipeline, or in the individual versions.yml files produced by each process.
Acknowledgments

We thank the developers and maintainers of all the open-source tools that make the SeqAudit pipeline possible. Special thanks to the Nextflow community and the Bioconda project for providing standardized, reproducible software environments.

## 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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