Can snippy detect large insertions?

Question

[ThePresident]

I was trying to find out this information in the snippy manual and elsewhere without success. What are the limits on insertion and deletions that snippy can detect? I feel it's on the lower end as I snippy could not detect insertion of about 1kb atb resistance cassette in my sample but detected a bunch of smaller SNPs and InDels.

What tools could be used to detect large insertions and deletion in bacterial (haploid and small) genomes?

Thanks, TP

[andres.firrincieli]

I do not think is possible to detect such a 1kb insertion with Snippy.

You should probably look for structural variant calling tools but since you have Illumina reads, 1kb insertions are difficult to find.

Alternatively, you could try to perform reassembly of the genome to identify the insertion site of the resistance cassette

[ThePresident]

Yeah, I came to the same conclusion. I think my only way forward is to assemble the genomes and use ACT with the caveat that it's all manual afterwards. I believe Mauve could do automate the job but I haven't used it since 2010 so...

[andres.firrincieli]

If you don't have to many genome mauve will do the job.