Kamil S. Jaron opened issue #181: comparing v3 vs v4 output at ezlab / busco

Kamil S. Jaron
2020-01-17T16:24:43Z

Hello again, I just looked at the BUSCO v4 (4.0.1) output and to my shock, I found that it find much less of the genes than v3 (3.0.2). Not sure if it's a result of newer version of orthologous set or newer version of busco itself, but fact remains that out of relatively reasonable busco results (86.9% complete) I got quite a crappy one (66.3% complete).

Is this expected? What is the interpretation? Should I try v4 busco with v9 OrthoDb? Or other way around? If interesting I can provide logs and/or additional info.

Commands and results:

run_BUSCO.py -i scaffolds.fasta -c 48 -o busco_v3 -m genome -t temp -l busco_dbs/arthropoda_odb9 -z
> C:86.9%[S:85.2%,D:1.7%],F:8.0%,M:5.1%,n:1066

busco -i scaffolds.fasta -c 48 -o busco_v4 -m genome -l arthropoda_odb10
> C:66.3%[S:65.3%,D:1.0%],F:7.3%,M:26.4%,n:1013