Question: BUSCO producing different genome completeness
0
gravatar for Mehmet
15 months ago by
Mehmet490
Japan
Mehmet490 wrote:

Dear All,

I would like to have your idea on a topic.

I run Busco (the latest version) for genomes of six worm species using eukaryote and nematoda database separately, and received different completeness results in one species. the species had ~92 % completeness when I run eukaryote database and ~77 % completeness when I run nematoda database. Other five species had very close completeness in eukaryote and nematoda database.

Do you have any idea what may explain this difference?

I run same command except lineage (database).

genome assembly gene • 639 views
ADD COMMENTlink modified 15 months ago by Chris Fields2.1k • written 15 months ago by Mehmet490

How are other metrics (N50, number of contigs / scaffolds, genome size, coverage, etc) for all six genomes? Is this particular genome more fragmented than the others? How many genes are included on the "Eukaryotes" and "Nematodes" sets?

First thing which springs to my mind is maybe it is not a nematode genome?

ADD REPLYlink written 15 months ago by h.mon27k
1
gravatar for Chris Fields
15 months ago by
Chris Fields2.1k
University of Illinois Urbana-Champaign
Chris Fields2.1k wrote:

This is expected; different taxonomic groups would have different single-copy orthologs (with more refined taxonomic groups having more SCOs compared to broader groups). Also, I know several nematode genomes have lower than expected BUSCO scores, which may be due to issues with assembly, etc.

ADD COMMENTlink written 15 months ago by Chris Fields2.1k
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