nf-core/pairgenomealign

nf-core/pairgenomealign

[![GitHub Actions CI Status](https://github.com/nf-core/pairgenomealign/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/pairgenomealign/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/pairgenomealign/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pairgenomealign/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pairgenomealign/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.13910535-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.13910535) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) [![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pairgenomealign) [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pairgenomealign-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pairgenomealign)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) ## 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](docs/images/pairgenomealign-tubemap.png "Tubemap workflow summary") 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](https://genome.ucsc.edu/FAQ/FAQformat.html#format5) 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](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) 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 \ --target sequencefile.fa \ --input samplesheet.csv \ --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](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files). For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pairgenomealign/usage) and the [parameter documentation](https://nf-co.re/pairgenomealign/parameters). ## Pipeline output To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pairgenomealign/results) tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/pairgenomealign/output). ## Credits `nf-core/pairgenomealign` was originally written by [charles-plessy](https://github.com/charles-plessy); the original versions are available at . We thank the following people for their extensive assistance in the development of this pipeline: - [Mahdi Mohammed](https://github.com/U13bs1125) ported the original pipeline to _nf-core_ template 2.14.x. - [Martin Frith](https://github.com/mcfrith/), the author of LAST, gave us extensive feedback and advices. - [Michael Mansfield](https://github.com/mjmansfi) tested the pipeline and provided critical comments. - [Aleksandra Bliznina](https://github.com/aleksandrabliznina) contributed to the creation of the initial `last/*` modules. - [Jiashun Miao](https://github.com/miaojiashun) and [Huyen Pham](https://github.com/ngochuyenpham) tested the pipeline on vertebrate genomes. ## Contributions and Support If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). For further information or help, don't hesitate to get in touch on the [Slack `#pairgenomealign` channel](https://nfcore.slack.com/channels/pairgenomealign) (you can join with [this invite](https://nf-co.re/join/slack)). ## 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](https://doi.org/10.1101/gr.278295.123). PubMed ID: [38621828](https://pubmed.ncbi.nlm.nih.gov/38621828/) [OIST research news article](https://www.oist.jp/news-center/news/2024/4/25/oikopleura-who-species-identity-crisis-genome-community) And also please cite the [LAST papers](https://gitlab.com/mcfrith/last/-/blob/main/doc/last-papers.rst). An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](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](https://dx.doi.org/10.1038/s41587-020-0439-x).

License
MIT

Contents

  • ["nf-core/pairgenomealign"]
  • assets/
  • conf/
  • docs/
  • docs/images/
  • modules/
  • modules/local/
  • modules/nf-core/
  • workflows/
  • subworkflows/
  • nextflow.config
  • README.md
  • nextflow_schema.json
  • CHANGELOG.md
  • LICENSE
  • CODE_OF_CONDUCT.md
  • CITATIONS.md
  • modules.json
  • docs/usage.md
  • docs/output.md
  • .nf-core.yml
  • .pre-commit-config.yaml
  • .prettierignore