Comments (1)
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.
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Related Issues (20)
- read mapping multiple references? HOT 1
- conda install failed HOT 3
- results filter for antibiotic resistance genes HOT 3
- KeyError with one header in CARD HOT 1
- Please port to Python3 HOT 2
- Same output entries from db HOT 1
- VFDB cannot be executed from the middle.
- databases not updated HOT 1
- Different naming from Resfinder CGE db HOT 3
- Clustering CARD database HOT 4
- password request HOT 1
- Gene typing gene results contain last hit of the list and not the best hit
- "ecoli.txt" HOT 1
- srst2_and_bowtie2 HOT 1
- Neisseria Gonorrhoeae
- output
- urllib2.URLError:
- SyntaxError when running srst2 HOT 1
- Indel variation in reference alleles lead to sporadic ST miscalls for S. aureus
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