Run Phyloflash with custom database?

HRGV / phyloFlash

phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.

GNU General Public License v3.0

75 stars 25 forks source link

Run Phyloflash with custom database? #172

Open whitnersyrena opened 1 year ago

whitnersyrena commented 1 year ago

I am hoping to run Phyloflash with a different database than SILVA - specifically the PR2 database instead. I am wondering if this has been done/is possible? If so please advise!

Thanks, Syrena

kbseah commented 1 year ago

Sorry for the late response You can 'hack' a third party database to the SILVA format, following instructions here: https://hrgv.github.io/phyloFlash/install.html (section 4.3) It should be possible to write a script to reformat the headers in one of the PR2 flat files to do so. We plan to improve support for custom databases in a new version, but this entails a complete rewrite and will take at least several months.