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theiagen / public_health_bacterial_genomics

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amrfinderplus improvements #210

Open kapsakcj opened 1 year ago

kapsakcj commented 1 year ago

Based on this info: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus#input-file-formats

I think the amrfinderplus task can be improved greatly if we provide it a GFF as well as a protein FASTA along side the nucleotide FASTA (assembly).

We could alter the workflows to:

kapsakcj commented 1 year ago

There's a bit more explanation here: https://github.com/ncbi/amr/wiki#methods

(and probably in the publications too, which I need to read)

but this could help identify novel sequences

for example...novel shiga toxin genes produced by STECs

kapsakcj commented 1 year ago

Now that v3.11.2 is available in a staphb docker image, we also need to make changes to the amrfinderplus task to accept new organism designations:

"Klebsiella_pneumoniae" and "Klebsiella_oxytoca"

"Neisseria_gonorrhoeae" and "Neisseria_meningitidis"

More details: https://github.com/StaPH-B/docker-builds/issues/550#issuecomment-1386035135