# nf-core/pairgenomealign

#

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Genome QC ([`assembly-scan`](https://github.com/rpetit3/assembly-scan)). 2. Genome indexing ([`lastdb`](https://gitlab.com/mcfrith/last/-/blob/main/doc/lastdb.rst)). 3. Genome pairwise alignments ([`lastal`](https://gitlab.com/mcfrith/last/-/blob/main/doc/lastal.rst)). 4. Alignment plotting ([`last-dotplot`](https://gitlab.com/mcfrith/last/-/blob/main/doc/last-dotplot.rst)). 5. Alignment export to various formats with [`maf-convert`](https://gitlab.com/mcfrith/last/-/blob/main/doc/maf-convert.rst), plus [`Samtools`](https://www.htslib.org/) 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](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