mnshgl0110
commented
5 months ago Ideally, syri requires the two genomes to have homologous chromosomes. In your case, that would mean comparing 1 plasmid to its homologous counterpart among the three plasmids from the other genome. If you want nt to do this, then you can just filter out the non homologous contigs either manually or using fixchr.
You can also consider concatenating the three plasmids to get one long plasmid and then running the syri pipeline. But this would be a bit less elegant and require some post-processing of syri output.
On Tue, Jan 16, 2024, 12:52 AM Michael Hall @.***> wrote:
This is a really awesome tool. I would love to be able to use it more generally on bacterial genomes. It works great if I have the same number of contigs, but sometimes I want to align two genomes where one genome might have 3 plasmids and the other genome might only have 1.
Is there a way to deal with this in syri already? Or is this something when you can add a flag that says ignore contigs that don't align. In my example the names of the contigs aren't necessarily going to be the same.
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mbhall88
This is a really awesome tool. I would love to be able to use it more generally on bacterial genomes. It works great if I have the same number of contigs, but sometimes I want to align two genomes where one genome might have 3 plasmids and the other genome might only have 1.
Is there a way to deal with this in syri already? Or is this something when you can add a flag that says ignore contigs that don't align. In my example the names of the contigs aren't necessarily going to be the same.