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https://github.com/nschan/nf-plotsv
Compare genomes using minimap2, SyRi and plotsr in a nextflow pipeline
https://github.com/nschan/nf-plotsv
Last synced: 8 days ago
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Compare genomes using minimap2, SyRi and plotsr in a nextflow pipeline
- Host: GitHub
- URL: https://github.com/nschan/nf-plotsv
- Owner: nschan
- License: mit
- Created: 2024-09-05T13:32:29.000Z (2 months ago)
- Default Branch: main
- Last Pushed: 2024-09-12T14:30:32.000Z (2 months ago)
- Last Synced: 2024-09-13T01:41:46.687Z (2 months ago)
- Language: Nextflow
- Size: 43.9 KB
- Stars: 2
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# nf-plotsv
This [`nextflow`](https://nextflow.io) pipeline can be used to analyze genomes using [`syri`](https://schneebergerlab.github.io/syri/) and [`plotsr`](https://github.com/schneebergerlab/plotsr/). Whole genome alignments are created using minimap2, oriented and re-alinged if needed, and then passed to syri and then to plotsr.
This pipeline by default uses [`plotsr`](https://github.com/schneebergerlab/plotsr/), which is a nice tool. Since I prefer `R` for plotting, I have created a parser for syri output that can be used to plot syri output via the excellent [`gggenomes`](https://github.com/thackl/gggenomes) package. If this sounds interesting, have a look here: https://github.com/nschan/syri_gggenomes
# Usage
After cloning into `$HOME` this pipeline can be run locally with `conda` environments like this:
```
nextflow run ~/nf-plotsv --samplesheet samplesheet.csv -profile local,conda
```
> NB: Since there is no conda package for fixchr, fixchr only works with containers.
Or locally with docker
```
nextflow run ~/nf-plotsv --samplesheet samplesheet.csv -profile local,docker
```
Or on biohpc_gen@LRZ using charliecloud
```
nextflow run ~/nf-plotsv --samplesheet samplesheet.csv -profile biohpc_gen,charliecloud
```
To run on other infrastructure, a matching config needs to be created (or copied from [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf))
## Samplesheet
Samplesheet layout is
```
name,fasta
```
Reference name can be provided using `--reference`, reference genome path is `--ref_genome`.
> Note: The reference genome needs to be prefiltered to contain the same chromsomes as those selected using `params.subset_pattern` when **not** using pairwise mode
## Params
Default params are defined in [`nextflow.config`](nextflow.config):
| Parameter | Effect | Default |
| --- | --- | --- |
| samplesheet | Samplesheet to be used | `false` |
| reference | Reference Name | `'Col-CEN_v1.2'` |
| ref_genome | Referemce genome fasta | `'$projectDir/assets/Col-CEN_v1.2.fasta'` |
| reorient | Reorient sequences to have them all go the same direction? This option does not work with `-profile conda` | `false` |
| pairwise | Use pairwise mode (see below) | `true` |
| subset_pattern | Pattern used for subsetting genomes in samplesheet | `"Chr[1-5]"` |
| out | Directory for results | `'./'` |
| plotsr_conf | Config file for plotsr | `"$projectDir/assets/plotsr_config.conf"` |
| plotsr_args | Extra arguments for plotsr | `'-S 0.7 -W 5 -H 5 -f 12'` |
| plotsr_tracks | path to tracks file for plotsr, see [here](https://github.com/schneebergerlab/plotsr/blob/master/README.md#visualising-tracks). | `''` |
| plotsr_colors | Color palette to use. | [alphabet palette](https://kwstat.github.io/pals/reference/discrete.html) |
> plotsr_tracks needs to be a full path, e.g. something like "$PWD/tracks.txt" should work.
> plotsr_colors need to be provided as hex, see nextflow.config
### Pairwise mode
`--pairwise`: create consecutive pairwise alignments from the samplesheet to create a plot across many genomes.
This will create pairwise alignments from top to bottom of the samplesheet (i.e. align row2 on row1, row3 on row2, row4 on row3, etc) and then create a _single_ plot using plotsr.
### plotsr
`plotsr` is controlled via a config file. Defaults to the one in `assets/`
# Pipeline graph
```mermaid
%%{init: {'theme': 'dark',
'themeVariables':{
'commitLabelColor': '#cccccc',
'commitLabelBackground': '#434244',
'commitLabelFontSize': '12px',
'tagLabelFontSize': '12px',
'git0': '#8db7d2',
'git1': '#58508d',
'git2': '#bc5090',
'git3': '#ff6361',
'git4': '#ffa600',
'git5': '#74a892',
'git6': '#d69e49',
'git7': '#00ffff'
},
'gitGraph': {
'mainBranchName': "Prepare Genome",
'parallelCommits': false
}
}
}%%
gitGraph TB:
commit id: "Subset by name [--subset_pattern]"
commit id: "Alignment"
commit id: "Identify / reorient misoriented [--reorient]"
branch "Align"
checkout "Align"
commit id: "Align sequences"
branch "SyRi / plotsr"
checkout "SyRi / plotsr"
commit id: "Run SyRi"
commit id: "Plot results"
```
# Software used
This pipeline uses the following packages:
- [`minimap2`](https://github.com/lh3/minimap2)
- [`seqtk`](https://github.com/lh3/seqtk)
- [`seqkit`](https://bioinf.shenwei.me/seqkit/)
- [`syri`](https://schneebergerlab.github.io/syri/)
- [`fixchr`](https://github.com/schneebergerlab/fixchr)
- [`plotsr`](https://github.com/schneebergerlab/plotsr)
# Cite
- Goel, M., Sun, H., Jiao, WB. et al. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol 20, 277 (2019). https://doi.org/10.1186/s13059-019-1911-0
- Goel M, Schneeberger K. plotsr: visualizing structural similarities and rearrangements between multiple genomes. Bioinformatics. 2022 May 13;38(10):2922-2926. doi: 10.1093/bioinformatics/btac196
- Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018 Sep 15;34(18):3094-3100. doi: 10.1093/bioinformatics/bty191
- Shen W, Le S, Li Y, Hu F. SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS One. 2016 Oct 5;11(10):e0163962. doi: 10.1371/journal.pone.0163962