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AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/
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Some AMR genes don't are detected in my contigs data. #146

Closed MicSonn closed 3 months ago

MicSonn commented 3 months ago

Hi,

Thanks for this very useful tool.

I run amrfinder v3.12.8 with db v2024-01-31.1 on Acinetobacter_baumannii as organism.

Some genes as adeA/adeB,.../adeS and mrcB and some others don't are detected. If I Run Blastn on my contigs the above genes are detected properly.

Could you help me understand why?

Best regards, Michele

vbrover commented 3 months ago

Are you using the --plus option?

MicSonn commented 3 months ago

Yes, --plus and --mutation_all --threads 15

vbrover commented 3 months ago

Could you post the input files and the complete AMRFinderPlus command you are using?

MicSonn commented 3 months ago

amrfinder --threads 15 --plus --name Acinetobacter --nucleotide contigs.fasta --organism Acinetobacter_baumannii --output ./ --mutation_all ./mut.txt --nucleotide_output ./nucl.txt

The multifasta file and Data Analysis are being published, I can't share it for the moment. However, it is correctly formatted as a multifasta as SPades output. In total, 30 samples were analyzed.

vbrover commented 3 months ago

Some genes as adeA/adeB,.../adeS and mrcB and some others don't are detected. If I Run Blastn on my contigs the above genes are detected properly.

Are these genes in the AMRFinderPlus database?

MicSonn commented 3 months ago

I haven't checked the db, I imagine these genes are not present. In fact my question is why aren't they present?

I'll check the db carefully

MicSonn commented 3 months ago

Thanks for now, see you tomorrow.

evolarjun commented 3 months ago

The AMRFinderPlus database should cover known phenotypically important acquired AMR genes and notable virulence and stress resistance genes for certain curated taxa. A full list of the genes included in AMRFinderPlus can be seen in the Reference Gene Hierarchy at https://www.ncbi.nlm.nih.gov/pathogens/genehierarchy/

The Reference Gene Catalog at https://www.ncbi.nlm.nih.gov/pathogens/refgene/ lists all protein references and point mutations included in the database.

MicSonn commented 3 months ago

Perfect!!! Thank you very much