How to find orthologs in both complete and fragmented genomes using OMA Standalone ?

Question

[amandinette]

Hi,

I would like to identify orthologs among about 40 bacterial genomes and then construct an orthologous matrix. Some of the genomes I am working on have been retrieved from the NCBI website and are complete. Others are custom genomes with an assembly level being "scaffolds".

I tried to use the "OMA Standalone" tool. I set "UseEsprit := true;" because of the fragmented assemblies of the custom genomes. It works until the end but no orthologous matrix was created at the end.

Is there a way to construct an orthologous matrix with both complete and fragmented genomes using OMA Standalone ?

Many thanks in advance if you can help me ! Best regards, Amandine

Answer 1

[Christophe Dessimoz]

Although OMA standalone and ESPRIT run within the same software, they have different purposes and for the moment we don't provide a unified pipeline between the two. This means that you have to take a two step process:

1. Run ESPRIT to identify likely split genes (which is what you appear to have done). Based on the output—and I recommend starting by only considering the high-confidence "hits.txt" output file—generate a new fasta file with merged fragments. You need to do this last step by yourself—we currently don't provide a tool for this.
2. Run the OMA algorithm (i.e. with UseEsprit := false) on the reference proteomes and updated fasta files with merged fragments. For this, you can keep the genomes that have not changed in the DB directory, and replace the scaffold-quality genomes (with filename .contig.fa) by their improved version from the ESPRIT output (make sure that the names are distinct).

[amandinette]

Thank you for these explanations !

[WouterDeCoster]

If this answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

[amandinette]

done ! (sorry, I am a newbie on this forum :-) )

[WouterDeCoster]

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