NEW FEATURE: synteny

[FernandoDuarteF]

Add synteny analysis and synteny plots.

[chriswyatt1]

Find a simple program to run this analysis. To get dotplots

[mr-eyes]

I would suggest the ModDotPlot for self-alignments. (if this fits the context here).

[chriswyatt1]

Cool, yeah we can take a look. But happy for any program to be added. Maybe it needs an nf-core module for it

[chriswyatt1]

@FernandoDuarteF suggests https://mummer.sourceforge.net/manual/
Nucmer

Typical commands:

nucmer -p aln ref.fa query.fa
delta-filter -r -q aln.delta > aln.filtered.delta
mummerplot --png -p dot aln.filtered.delta

Output: dot.png

nucmer aligns genomes

mummerplot generates the dotplot image

[chriswyatt1]

Or : https://github.com/genotoul-bioinfo/dgenies?tab=readme-ov-file
Is a one liner command we could make into an nf-core module.

[LiaOb21]

This is what I used when I needed a synteny analysis: https://github.com/schneebergerlab/syri

[chriswyatt1]

That looks great, and we can break it up into existing modules, minimap2, samtools view, syri and nucmer. So we just need to create a syri module.

Reignite this issue:

nf-core/modules#5658 for the main run command,

PLus another module for plot

python3 $PATH_TO_PLOTSR syri.out refgenome qrygenome -H 8 -W 5

Here are the docs:
https://schneebergerlab.github.io/syri/pipeline.html

[chriswyatt1]

Maybe it makes to make this a subworkflow

[LiaOb21]

There is a module for syri https://github.com/nf-core/modules/blob/master/modules/nf-core/syri :)

Edit: there is also a module for plotsr https://nf-co.re/modules/plotsr/

[chriswyatt1]

I made a subworkflow: https://github.com/chriswyatt1/modules/tree/Add_subworkflow_syri . Which I could try to merge into nf-core subworkflows

But it only does pairs of genome separately. But at least for now, this may be useful to add to the pipeline.