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pairgenomealign

Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results

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

Science Score: 67.0%

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    CITATION.cff file
    Found CITATION.cff file
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    Found codemeta.json file
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    Found .zenodo.json file
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    DOI references
    Found 10 DOI reference(s) in README
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    Links to: pubmed.ncbi, ncbi.nlm.nih.gov
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    Low similarity (10.0%) to scientific vocabulary

Keywords

bioinformatics comparative-genomics dot-plot genomics last nextflow nf-core pairwise-alignment synteny whole-genome-alignment
Last synced: 6 months ago · JSON representation ·

Repository

Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results

Basic Info
Statistics
  • Stars: 9
  • Watchers: 178
  • Forks: 5
  • Open Issues: 12
  • Releases: 7
Topics
bioinformatics comparative-genomics dot-plot genomics last nextflow nf-core pairwise-alignment synteny whole-genome-alignment
Created over 1 year ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nf-core/pairgenomealign

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

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

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Introduction

nf-core/pairgenomealign is a bioinformatics pipeline that aligns one or more query genomes to a target genome, and plots pairwise representations.

Tubemap workflow summary

The main steps of the pipeline are:

  1. Genome QC (assembly-scan).
  2. Genome indexing (lastdb).
  3. Genome pairwise alignments (lastal).
  4. Alignment plotting (last-dotplot).
  5. Alignment export to various formats with maf-convert, plus Samtools for SAM/BAM/CRAM.

The pipeline can generate four kinds of outputs, called many-to-many, many-to-one, one-to-many and one-to-one, depending on whether sequences of one genome are allowed match the other genome multiple times or not.

These alignments are output in MAF format, and optional line plot representations are output in PNG format.

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,fasta query_1,path-to-query-genome-file-one.fasta query_2,path-to-query-genome-file-two.fasta

Each row represents a fasta file, this can also contain multiple rows to accomodate multiple query genomes in fasta format.

Now, you can run the pipeline using:

bash nextflow run nf-core/pairgenomealign \ -profile <docker/singularity/.../institute> \ --target sequencefile.fa \ --input samplesheet.csv \ --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/pairgenomealign was originally written by charles-plessy; the original versions are available at https://github.com/oist/plessy_pairwiseGenomeComparison.

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

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 #pairgenomealign channel (you can join with this invite).

Citations

If you use this pipeline, please cite:

Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species. Charles Plessy, Michael J. Mansfield, Aleksandra Bliznina, Aki Masunaga, Charlotte West, Yongkai Tan, Andrew W. Liu, Jan Grašič, María Sara del Río Pisula, Gaspar Sánchez-Serna, Marc Fabrega-Torrus, Alfonso Ferrández-Roldán, Vittoria Roncalli, Pavla Navratilova, Eric M. Thompson, Takeshi Onuma, Hiroki Nishida, Cristian Cañestro, Nicholas M. Luscombe. Genome Res. 2024. 34: 426-440; doi: 10.1101/2023.05.09.539028. PubMed ID: 38621828

OIST research news article

And also please cite the LAST papers.

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/pairgenomealign: 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 design

> Charles Plessy, Michael J. Mansfield, Aleksandra Bliznina, Aki Masunaga, Charlotte West, Yongkai Tan, Andrew W. Liu, Jan Grašič, María Sara del Río Pisula, Gaspar Sánchez-Serna, Marc Fabrega-Torrus, Alfonso Ferrández-Roldán, Vittoria Roncalli, Pavla Navratilova, Eric M. Thompson, Takeshi Onuma, Hiroki Nishida, Cristian Cañestro, Nicholas M. Luscombe. Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species. Genome Res. 2024. 34: 426-440; doi: [10.1101/2023.05.09.539028](https://doi.org/10.1101/gr.278295.123). PubMed ID: [38621828](https://pubmed.ncbi.nlm.nih.gov/38621828/)

## Pipeline tools

- [LAST](https://gitlab.com/mcfrith/last/)

  > Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 21(3):487-93. doi: 10.1101/gr.113985.110. PubMed PMID: 21209072 (This describes the main algorithms used by LAST.)

  > Frith MC, Noé L. Improved search heuristics find 20,000 new alignments between human and mouse genomes. doi: 10.1093/nar/gku104 PubMed PMID: 24493737 (This describes sensitive DNA seeding (MAM8 and MAM4)

  > Frith MC, Kawaguchi R. Split-alignment of genomes finds orthologies more accurately. Genome Biology. 2015 16:106. doi: 10.1186/s13059-015-0670-9 PubMed PMID: 25994148 (Describes the split alignment algorithm, and its application to whole genome alignment.)

  > Hamada M, Ono Y, Asai K Frith MC. Training alignment parameters for arbitrary sequencers with LAST-TRAIN. Bioinformatics. 2017 33(6):926-928. doi: 10.1093/bioinformatics/btw742 PubMed PMID: 28039163 (Describes last-train.)

  > Frith MC, Shaw J, Spouge JL. How to optimally sample a sequence for rapid analysis. doi: 10.1093/bioinformatics/btad057 PubMed PMID: 36702468 (Describes the lastdb -u RY sparsity options.)

- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)

  > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.

- [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.

## 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: 19
  • Release event: 5
  • Issues event: 61
  • Watch event: 2
  • Delete event: 13
  • Issue comment event: 46
  • Push event: 78
  • Pull request review comment event: 74
  • Pull request review event: 72
  • Pull request event: 40
  • Fork event: 2
Last Year
  • Create event: 19
  • Release event: 5
  • Issues event: 61
  • Watch event: 2
  • Delete event: 13
  • Issue comment event: 46
  • Push event: 78
  • Pull request review comment event: 74
  • Pull request review event: 72
  • Pull request event: 40
  • Fork event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 35
  • Total pull requests: 20
  • Average time to close issues: 2 months
  • Average time to close pull requests: 15 days
  • Total issue authors: 7
  • Total pull request authors: 2
  • Average comments per issue: 0.31
  • Average comments per pull request: 0.25
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 35
  • Pull requests: 20
  • Average time to close issues: 2 months
  • Average time to close pull requests: 15 days
  • Issue authors: 7
  • Pull request authors: 2
  • Average comments per issue: 0.31
  • Average comments per pull request: 0.25
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • charles-plessy (32)
  • jonasscheid (1)
  • katherinermartin (1)
  • SamCT (1)
  • jen-reeve (1)
  • ryandkuster (1)
  • cahuparo (1)
  • edmundmiller (1)
Pull Request Authors
  • charles-plessy (23)
  • nf-core-bot (9)
  • U13bs1125 (3)
  • mashehu (1)
  • jantmo (1)
Top Labels
Issue Labels
enhancement (22) bug (12)
Pull Request Labels
bug (2) enhancement (1)

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