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arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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New metagenomics statistic #279

Open agmcarthur opened 2 months ago

agmcarthur commented 2 months ago

Playing with some bait-capture enriched ARG metagenomics data with RGI bwt with KMA and all the wildcard variants and looking at the gene level report, I found tet(Q) with All Mapped Reads = 41863 but Average Percent Coverage = 21.25. The latter is because there was Alleles with Mapped Reads = 83 and most alleles because of KMA had few reads. KMA appropriately aligned most reads to the correct allele, which had 100% coverage of that reference sequence. I think we need a new Maximum Observed Allelic Coverage column in the gene report so we don't have to mine the allelic report. Or perhaps some best allele columns for All Mapped Reads and Percent Coverage?

github-actions[bot] commented 1 week ago

Issue is stale and will be closed in 7 days unless there is new activity

agmcarthur commented 1 week ago

A bit on the backburner while we work on other RGI code.