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ammaraziz / ctgap

Chlamydia trachomatis Genome Assembly Pipeline
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Add snippy for SNP detection #16

Open gokeson opened 4 months ago

gokeson commented 4 months ago

Add snippy to detect snps between multiple assembly methods.

We should be able to have this feature for between sample comparisons too. What do you think?

So, we will have

ammaraziz commented 4 months ago

This is for inclusion into ctgap or a separate comparison workflow?

gokeson commented 4 months ago

This is for inclusion into ctgap or a separate comparison workflow?

A separate comparison workflow. I don’t readily see the need to include this in the main ctgap workflow.

luclzhu commented 1 month ago

I've implemented snp detection using dnadiff from mummer for comparison between assembly methods only as of now.

It seems more challenging to compare between sequences with dnadiff or snippy since both can only compare 2 seqeunces at a time. One way I can think of to get around this is comparing each sequence to a reference sequence, then combining all those results (maybe with multiqc?)