Run iphop only on host lineages of interest

[Anneliek ter Horst]

Hi Simon,

Really like this tool, but the database is really big. I was wondering if there is a way that I can only run iphop on host genomes of interest, for example only on hosts with a specific taxonomic lineage (only E. coli species, or only Methanomicrobiales).

Would there be a way to subset the database in such a way?

[Simon Roux]

Hi !
Right, the database is big and that makes the compute that much longer. Unfortunately, iPHoP relies a lot of these “non-host” similarities to identify potential hosts, i.e. potential hosts are detected based on “microbial genomes that stand out compared to everything else”, so I have not found a good way to reduce / subset the host database at this point :-(

Best,

Simon

[Anneliek ter Horst]

Ah, makes sense!

Thank you!!