PPR-Meta scoring

[hoelzer]

Currently, all sequences are considered as viruses that are reported as "phages" by PPR-Meta. However, we can additionally filter by a "phage score" provided by the tool:

Header,Length,phage_score,chromosome_score,plasmid_score,Possible_source
seq8,86578,0.658026557109837,0.323770475766357,0.0182029599535136,phage
seq11,63443,0.671362450565434,0.257167359821571,0.0714701900259453,phage
seq20,41715,0.945974168353953,0.0147801588566125,0.0392456778921355,phage
seq22,38841,0.999412552439551,1.51951318980135e-05,0.000572250124745809,phage

awk 'BEGIN{FS=","}{if($6=="phage" && $3>0.7){print $0}}' 01-viruses/pprmeta/kleiner_virome_2015_pprmeta.csv 

This is also done here

[hoelzer]

I checked this for the Kleiner and Neto data set. Kleiner is not affected at all (because we combine PPRmeta results with VF results anyway) but some changes for Neto:

For Neto we reduce the number of unclassified contigs from 105 to 92. We also lose some Imitervirales annotations though.

[hoelzer]

I would still do this and implement a parameter for the PPR-Meta filtering and not just taking all hits that are phage into account. A good default seems >0.7