Jared Simpson

When align2alleles.py is called with --min-allele-count > 1 and a SNP is present in all samples, the reference allele will not be included here: https://github.com/jts/ncov-tools/blob/master/workflow/scripts/align2alleles.py#L82 This is not unintuitive so...

Hi, Thanks for providing this tool, it is very useful. I have been testing it on nanopore data and noticed a potential issue in the modbam parser. In the current...

Question: dump sequences of hetmers

3

Hi, Thanks for developing smudgeplot, I've found it to be very useful. I would like to do a deeper analysis of the results, which requires the sequences of each A/B...

Hi, It seems there are some typos in the implementation of IUPAC ambiguity codes before calling edlib: https://github.com/nanoporetech/pipeline-umi-amplicon/blob/master/lib/umi_amplicon_tools/extract_umis.py#L118 For example `("R", "A"), ("R", "A")` should be `("R", "A"), ("R", "G")`...