how to run the tool agains multiple inputs

[Overcraft90]

Hi there,

I pretty much understood how to run the tool for a single genome to reference alignment and set up a script to align both hap1 and hap2 of a plant species against the reference to then run Syri. However, my understanding of this is that the plotsr will then show only the reference and one haplotype for each sample in the visualization for all the 25 chromosomes of this species

What I want instead is an alignment of all hap1 for each one of the 16 samples we assembled as well as hap2 against the reference, and then have two separate plots for hap1 and hap2 showing the 16 samples against the reference with all chromosomes.

From what I got here, this can be achieved putting all FASTA for hap1 in one file – querygenome_hap1 – and all FASTA for hap2 in another – querygenome_hap2 to then be processed with nucmer? Sorry for asking, but I have no experience with either tools; thanks in advance!

[lrauschning]

Hi,

the workflow for plotsr is to run any haplotype agains the one below it in the plot. If you want to compare two haplotypes against a common reference, you could e.g. align sample1_hap1 to ref + call syri and do the same for ref + sample1_hap2.
Have a look at the plotsr readme if you haven't already.
Plotsr purely uses the SyRI output, so you can use any aligner that produces a standard format syri can handle.
If you're interested in finding conserved structure across multiple genomes, it might also be worth taking a look at schneebergerlab/msyd, a tool that aggregates syri output and iteratively realigns structurally variable regions – though especially the second part is still in development.

Best,
Leon