Using GTDB-TK for a databas of partial bacterial genome

[mkoohim]

Hello,

I have a database biosynthetic gene cluster (BGCs) from different bacteria. BGCs are clusters of adjacent genes which is part of whole genome of the bacteria. I used GTDB-TK to make a phylogeny tree for these BGCs but unfortunately as its not whole genome I couldn't get any results and in identify step there was not any marker to match with these BGCs. I am wondering if there is any way to use GTDB-TK on these BGCs database? Ive attached here one of BGC file:

seq1.zip

[aaronmussig]

Hi, unfortunately the genome will need hits to marker genes since GTDB-Tk needs hits to either the 53, or 120 single-copy marker genes (for archaea and bacteria respectively).

You may be able to use the ani_rep command of GTDB-Tk to try and find the closest representative genome in ANI space, but note you may need a less-stringent alignment fraction value (this can be set with --min_af)

[pchaumeil]

Ticket closed due to inactivity.