Using srst2 for metagenomic screening

[Anto007]

Using srst2 for metagenomic screening

[katholt]

SRST2 is an allele typer, its scoring works on the assumption that there is a single allele present in the sample and aims to determine precisely what that one allele is. If there are multiple alleles present then the gene detection results are reliable, but the allele calling behaviour is unpredictable and meaningless if there is more than one allele present.
So, if you simply want to identify the presence of 'genes' without regard to the specific alleles then you could use SRST2 and just pay attention to the gene calls and ignore the specific allele calls.