Aligning & Comparing References for SNPs / Indels

Question

[jnowacki]

I have 6 viruses I want to compare for SNPs & INDELs. Favorite tools / methods to align and compare?

• No short reads.
• Only the assembled reference.
• 30kb in length x 6+ viruses
• SNP & INDEL export function preferred but not essential

Or am I stuck with run of the mill multiple sequence alignment and visual inspection?

Thanks,

Answer 1

[colindaven]

Have a look at pairwise tools like Mummer which can give you an optimal alignment. The file formats are somewhat ... strange ... though. By that I mean they are difficult to process further.

I would also look at multiple genome alignment (i.e. all six at once). Mugsy is one tool which works, and you can use the formats more easily downstream.

Potentially something new like vg or minigraph might be interesting.