kelwyres

Hi, It sounds like there might be a problem with your input reference sequence. BioPython is saying that the sequence is shorter than indicated in the record header. You can...

Hi Dyana, Looks like pipeline is trying to check the bam mapping outout but can't find the file- so that indicates something went wrong with the mapping step. What sort...

Hi, Great that you've managed to fix the SAMtools problem. Unfortunately, I don't think there is any way around the file name convention, so you'll need to rename them, or...

Hi, Yes, we think the database has pretty good coverage of the capsule diversity among Klebs pneumo species complex, so most low confidence calls are likely due to assembly issues...

Hi @stitam, You may have already seen, but we released the new version of Kaptive last week. It has higher sensitivity for genomes with fragmented K loci. Actually the code...

Hi Kathryn, It could be that the Kaptive submodule hasn't installed. Did you use the --recursive flag when you clones the kleborate github repo? (see here for explanation: https://github.com/katholt/Kleborate#installation) Kelly

Hi, Many apologies- there is a mistake on the Kaptive instructions page- Kaptive doesn't produce a Genbank file as output, only a fasta file. I will update the instructions page....

Hi Claire, Unfortunately we are currently having a few technical difficulties with the server and awaiting additional tech support. We're under stay at home orders here in Melbourne so it's...