srst2
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katholt
Short Read Sequence Typing for Bacterial Pathogens
Hello, Upon reviewing the fullgenes report after an allele typing run, I have noticed that multiple alleles of the same gene are listed, but the final gene results report doesn't...
Hi, I wanted to see if you could update SRST2 to show compatibility against the latest versions of bowtie2. There have been several versions since the last update of SRST2,...
Hi there, I am using SRST2 for a custom database to search for a small variable gene region (~320bp with flanking) within a set of _Campylobacter_ sp genomes. i have...
Hi, We (@nvlachos, @madgenetics, and I) ran into an issue with too many "." in the file names as described in #99 . In addition, in cases where a pileup...
I am reaching out in response to the recent communications with Alison Laufer Halpin ( and Jill Hagey) about trying to use srst2 in our pipeline. We have run into...
I have one isolate of C. diphtheriae that produces an unexpected allele call for one locus. Below is a filtered subset of the scores file, which indicates that allele dnaE_1...
Hello! I am trying to run srst2 in an HPC cluster to identify resistance genes and I get the error below: _Traceback (most recent call last): File "/CCAS/home/cpavloudi/miniconda3/bin/srst2", line 5,...
Hi, I am studying within-person S.aureus variability, and sequence many isolates to characterize the population diversity. I observe sporadically ST inconsistencies, where single isolates are called NF while other isolates...
Hi, I am running srst2 v0.2.0 in a conda environment and when I run `getmlst.py --species "Escherichia coli#1"` got the following error: ``` urllib2.URLError: ``` I found this error in...
My output file *_genes*results.txt only give one sample name,i don't know why . And My *fullgenes*results.txt has result , what's the "divergence"meaning?It's 12.164 means sample ARG gene's difference between reference...
