nf-plotsv

This nextflow pipeline can be used to analyze genomes using syri and 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, 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 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)

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:

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.	''
plotsr_colors	Color palette to use.	alphabet palette

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

%%{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"

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Software used

This pipeline uses the following packages:

• minimap2

• seqtk

• seqkit

• syri

• fixchr

• 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