Screening for mitochondrion

[wharvey31]

Hello,

We are running FCS on a set of genomes before submission to NCBI. We use the following command:

python3 fcs.py --image {fcs_img} screen genome --fasta {input.asm_fasta} --gx-db {params.GXDB_LOC}  --tax-id 9606

and are able to identify the same contamination as NCBI for the most part. What we are apparently missing is mitochondrion. Is there a parameter I am missing to flag this?

Thanks so much for the direction!

[etvedte]

Hello,

We are actively investigating the identification of organelle hits with FCS-GX, and this should be available in an upcoming release. Unfortunately I can't give a timeline of when this will be available, so for now I would rely on other methods to identify mitochondrial sequences.

Eric

[wharvey31]

Thanks for the reply!

So the internal version of fcs which is used to screen assemblies for submission is different than what is listed here? Is that correct?

[etvedte]

Yes, this is correct.

The current FCS-GX release matches closely to that individual component of our internal screening, but the internal screen also has some additional functionality (e.g. the organelle ID) that we haven't distributed to the public tool yet. The ultimate goal of this project will be to unify those two pipelines such that running FCS on your own will recapitulate our internal screen results.

[wharvey31]

Thanks so much! We would appreciate that well.

[gunjanpandey]

Thanks @etvedte and @wharvey31

We also eagerly wait for organelle genomes to be included in the gxdb as contaminants.