andrewjmc

That's a great question and embarrassingly demonstrates my question was ill informed! I assumed GTDB had to have its own stable IDs since NCBI genera, species etc can be split...

Long story... we have shotgun metagenomic data, and want to estimate carriage proportion of antibiotic resistance genes within genera. We have kraken RAs based on full GTDB sequences, but this...

Thanks. 180 G available. I was cheating here and just testing on a shared node. I was also just running mmseqs myself from the command line (but SemiBin does the...

OK, I'll try that thanks!

Just to add as a test case, I have provided a fastq sequence file with three reads ``` @K00150:405:HGVM5BBXY:6:2119:16741:38381/1 ATGAAATTCCATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGAAATTCCATGGAATGGAATGGAATGGAAAAGAATGGAATGGAATGAAATTCCATGGAATGGAATGGAATGGAATGGAATGAAATTCC + AAAFFJJJJJFAJJJJFJAFAAFJJFAFFJJAJJFF-FJAJ

Thanks to `trace(weightit, edit=TRUE)` I added some debug output and found that my smallest group (n=94 / 527) has `test.w` of 0, so `0 / 0` doesn't work When using...

Thanks!

In addition, do you have any sense of how runtime and memory usage scales (I appreciate that may depend on sequence redundancy)?

Super, thanks!

Manu, I was just thinking the same thing! In the manual, instructions are given to manually generate the data for bracken using kraken, and no confidence threshold is specified. It...