All-against-all mappings

[iminkin]

Hi,

Suppose that I have N long genomes (e.g. primates) and want to compute mappings between all pairs of the genomes. What is the best way to do so using mashmap? For example, is it a good idea to cat everything into a single FASTA file and then align it against itself, or it is the best to run the comparisons separately? And how would one adjust the parameters in such a case?

[cjain7]

You could go with either way... With the first approach, you may need additional post-processing of discarding mappings that span two genomes (in case they occur), so may be second is more convenient. Just pick the filtering criteria based on your application needs.