New feature request: Integrate NCBI FCS-adaptor into funannotate clean?

[IanDMedeiros]

Now that NCBI had released their internal adapter contamination screening tool for public use (https://ncbiinsights.ncbi.nlm.nih.gov/2022/07/28/fcs-beta-tool/), would it be possible to add an option for FCS-adaptor to be run as part of funannotate clean?

[hyphaltip]

patches always welcome - we also put more cleaning stuff in AAFTF stajichlab/AAFTF#7 - one issue I saw was at leats in the version NCBI had at beginning requires huge database setup and in-memoryruns so this may not be useable expect on HPCs so need to be clear.

[IanDMedeiros]

I think the huge database is only for FCS-GX; the FCS-adaptor tool is small and runs quickly.

[hyphaltip]

oh that would be better - yeah that would be good to add in - just I think @nextgenusfs was thinking of separating assembly cleaning from annotation but let's see if we can get this integrated in. at least in AAFTF there is a vectrim step we can augment.

[nextgenusfs]

I think fine to add it in both places as long as install dependencies don't cause build issues.

[nextgenusfs]

I might recant about including: this looks to be a shell script running a container in either docker or singularity. https://github.com/ncbi/fcs/blob/main/dist/run_fcsadaptor.sh.

That won't package in conda very well I don't think.

On the surface it appears to do what we have been doing for awhile in AAFTF with a blast for adapters and automatically cleaning them. So would be easier to move that aaftf code here than deal with the docker/container issue.

[nextgenusfs]

For reference, we could integrate our "vecscreen" contig cleaner in funannotate clean, it seems to be doing very similar to what fcs-adapter is attempting to do (ie find contamination, remove and split contigs, etc). https://github.com/stajichlab/AAFTF/blob/main/AAFTF/vecscreen.py

[hyphaltip]

My thoughts exactly. I agree this is best thing to do.

On Tue, Aug 9, 2022 at 2:39 PM Jon Palmer ***@***.***> wrote: For reference, we could integrate our "vecscreen" contig cleaner in funannotate clean, it seems to be doing very similar to what fcs-adapter is attempting to do (ie find contamination, remove and split contigs, etc). https://github.com/stajichlab/AAFTF/blob/main/AAFTF/vecscreen.py — Reply to this email directly, view it on GitHub <#759 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAL5O2W6N4NUX4PP2E3KI3VYLFXJANCNFSM555435JQ> . You are receiving this because you commented.Message ID: ***@***.***>

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[nextgenusfs]

ncbi/fcs#5