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| <h1> | ||
| <picture> | ||
| <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-pairgenomealign_logo_dark.png"> | ||
| <img alt="nf-core/pairgenomealign" src="docs/images/nf-core-pairgenomealign_logo_light.png"> | ||
| </picture> | ||
| </h1> | ||
| # nf-core/pairgenomealign: Documentation | ||
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| [](https://github.com/nf-core/pairgenomealign/actions/workflows/ci.yml) | ||
| [](https://github.com/nf-core/pairgenomealign/actions/workflows/linting.yml)[](https://nf-co.re/pairgenomealign/results)[](https://doi:zenodo.XXXXXXX) | ||
| [](https://www.nf-test.com) | ||
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| [](https://www.nextflow.io/) | ||
| [](https://docs.conda.io/en/latest/) | ||
| [](https://www.docker.com/) | ||
| [](https://sylabs.io/docs/) | ||
| [](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pairgenomealign) | ||
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| [](https://nfcore.slack.com/channels/pairgenomealign)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core) | ||
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| ## Introduction | ||
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| **nf-core/pairgenomealign** is a bioinformatics pipeline that aligns a single or set of query genomes in csv format with a target genome to make a pairwise representation in dotplots. | ||
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| This pipeline usually takes in as an input a sample sheet in csv format which contain this set of queries or single query and align it pairwise with atarget genome in fasta or fa.gz format to make a dotplots representation of the paired alignment or alignments in case of multiple queries. | ||
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| <img src= "assets/tube_map.svg"> | ||
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| ## Outputs | ||
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| For each _query_ genome, this pipeline will align it to the _target_genome, post-process the alignments and produce dot plots visualisations at different steps of the | ||
| workflow. Each file contains a name suffix that indicates in which order they were created. | ||
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| - `.train` is the alignment parameters computed by `last-train` (optional) | ||
| - `m2m_aln` is the _**many-to-many**_ alignment between _target_ and _query_ genomes. (optional through the `--m2m` option) | ||
| - `m2m_plot` (optional) | ||
| - `m2o_aln` is the _**many-to-one**_ alignment regions of the _target_ genome are matched at most once by the _query_ genome. | ||
| - `m2o_plot` (optional) | ||
| - `o2o_aln` is the _**one-to-one**_ alignment between the _target_ and _query_ genomes. | ||
| - `o2o_plot` (optional) | ||
| - `o2m_aln` is the _**one-to-many**_ alignment between the _target_ and _query_ genomes (optional). | ||
| - `o2m_plot` (optional) | ||
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| ## Mandatory parameters | ||
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| * `--target`: path or URL to one genome file in FASTA format. It will be indexed. | ||
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| * `--input`: path to a sample sheet in comma-separated format with one header line`sample, fasta`, and one row per genome (ID and path or URL to FASTA file). | ||
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| — or — | ||
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| `--query`: path or URL to one genome file in FASTA format. | ||
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| ## Options | ||
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| * `--seed` selects the name of the [LAST seed][] The default (`YASS`) searches for “_long-and-weak similarities_” that “_allow for mismatches but not gaps_”. Among alternatives, there are `NEAR` for “_short-and-strong (near-identical) similarities_ … _with many gaps (insertions and deletions)_”, `MAM8` to find _“weak | ||
| similarities with high sensitivity, but low speed and high memory usage”_ | ||
| or `RY128` that “_reduces run time and memory use, by only seeking seeds at | ||
| ~1/128 of positions in each sequence_”, which is useful when the purpose of | ||
| running this pipeline is only to generate whole-genome dotplots, or when | ||
| sensitivity for tiny fragments may be unnecessary or undesirable. Setting | ||
| the seed to `PSEUDO` triggers protein-to-DNA alignment mode (experimental). | ||
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| * `--lastal_args` defaults to `-C2` and is applied to both | ||
| the calls to `last-train` and `lastal`, like in the [LAST cookbook][] | ||
| and the [last-genome-alignments][] tutorial. | ||
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| * `--lastal_extr_args` (default: `-D1e9`) is only passed to `lastal` and | ||
| can be used for arguments that are not recognised by `last-train`. | ||
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| * `--lastal_params`: path to a file containing alignment parameters | ||
| computed by [`last-train`][] or a [scoring matrix][]. If this option | ||
| is not used, the pipeline will run `last-train` for each query. | ||
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| * `--m2m`: (default: false) Compute and output the many-to-many alignment. | ||
| This adds time and can comsume considerable amount of space; use only | ||
| if you need that data. | ||
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| * `--o2m`: (default: false) Also compute the _**one-to-many**_ alignments | ||
| and dotplots. This is sometimes useful when troubleshooting the | ||
| preparation of diploid assemblies. | ||
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| * `--one_to_one_only`: do not copy the other alignments to the results | ||
| folder, thus saving disk space. | ||
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| * By default, `last-split` runs with `-m1e-5` to omit alignments with | ||
| mismap probability > 10<sup>−5</sup>, but this can be overriden with | ||
| the `--last_split_mismap` option. | ||
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| * `--last_split_args` defaults to empty value and is not very useful at the | ||
| moment, but is kept for backwards compatibility. It can be used to pass | ||
| options to `last-split`. Note that if you used `--m2m false` (which is | ||
| the default), the split parameters have to be passed in | ||
| `--lastal_extra_args` and have different names (see _split options_ in the | ||
| [lastal documentation][]). | ||
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| * The dotplots can be modified by overriding defaults and passing new | ||
| arguments via the `--dotplot_options` argument. Defaults and available | ||
| options can be seen on the manual page of the [`last-dotplot`][] program. | ||
| By default in this pipeline, the sequences of the _query_ genome are | ||
| sorted and oriented by their alignment to the _target_ genome | ||
| (`--sort2=3 --strands2=1`). For readability, their names are written | ||
| horizontally (`--rot2=h`). | ||
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| * Use `--skip_dotplot_m2m`, `--skip_dotplot_m2o`, `--skip_dotplot_o2o` | ||
| `--skip_dotplot_o2m` to skip the production of the dot plots that can be | ||
| computationally expensive and visually uninformative on large genomes with | ||
| shared repeats. File suffixes (see above) will not change. | ||
| * By default the LAST index is named `target` and the ouput files are named | ||
| from the query IDs. Use the `--targetName` option to provide a name | ||
| that will be used for the LAST index and that will be prefixed to the | ||
| query IDs with a `___` separator. | ||
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| [`lastal`]: https://gitlab.com/mcfrith/last/-/blob/main/doc/lastal.rst | ||
| [`last-dotplot`]: https://gitlab.com/mcfrith/last/-/blob/main/doc/last-dotplot.rst | ||
| [LAST seed]: https://gitlab.com/mcfrith/last/-/blob/main/doc/last-seeds.rst | ||
| [LAST cookbook]: https://gitlab.com/mcfrith/last/-/blob/main/doc/last-cookbook.rst | ||
| [`last-train`]: https://gitlab.com/mcfrith/last/-/blob/main/doc/last-train.rst | ||
| [LAST tuning]: https://gitlab.com/mcfrith/last/-/blob/main/doc/last-tuning.rst | ||
| [scoring matrix]: https://gitlab.com/mcfrith/last/-/blob/main/doc/last-matrices.rst | ||
| [lastal documentation]: https://gitlab.com/mcfrith/last/-/blob/main/doc/lastal.rst | ||
| [last-genome-alignments]: https://github.com/mcfrith/last-genome-alignments | ||
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| ## Fixed arguments (taken from the [LAST cookbook][] and the [LAST tuning][] manual) | ||
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| * The `lastdb` step soft-masks simple repeats by default, (`-c -R01`).It indexes both strands (`-S2`), which increases speed at the expense of memory usage. | ||
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| * The `last-train` commands runs with `--revsym` as the DNA strands play equivalent roles in the studied genomes, unless the `--read_align` option is selected. | ||
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| * `last-split` runs with `-fMAF+` to make it show per-base mismap probabilities, except in read alignment mode (see below). | ||
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| ## Usage | ||
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| > [!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. | ||
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| First, prepare a samplesheet with your input data that looks as follows: | ||
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| `samplesheet.csv`: | ||
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| ```csv | ||
| sample,fasta | ||
| Query_1,AEG588A1_S1_L002_R1_001.fasta | ||
| ``` | ||
| Each row represents a fasta file, this can also contain multiple rows to accomodate multiple query genomes in fasta format. | ||
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| 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> | ||
| ``` | ||
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| > [!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/usage/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). | ||
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| ## Pipeline output | ||
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| 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). | ||
| The nf-core/pairgenomealign documentation is split into the following pages: | ||
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| - [Usage](usage.md) | ||
| - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags. | ||
| - [Output](output.md) | ||
| - An overview of the different results produced by the pipeline and how to interpret them. | ||
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| You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re) |