AMR annotations on chromsome?

apcamargo / genomad

geNomad: Identification of mobile genetic elements

https://portal.nersc.gov/genomad/

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AMR annotations on chromsome? #97

Open sophiaaredas opened 6 months ago

sophiaaredas commented 6 months ago

geNomad is such a great and powerful tool that has been especially helpful in my metagenomic analysis in regards to AMR and phage annotations. I noticed that the AMR genes that are output by geNomad are only found on the plasmid but I was wondering if it would ever be possible in the future to know what kinda of AMR genes are located on the chromosome? Thank you so much!

apcamargo commented 6 months ago

You can find the AMR annotations of all input sequences in the <prefix>_annotate/<prefix>_genes.tsv file. Genes with AMR annotation will be indicated in the annotation_amr column.