Torsten Seemann
Torsten Seemann
I think supporting IUPAC codes in some manner would be a good option to include, but it is complicated. What about d(W,W) and d(W, B/D/G/V) etc? ``` Nucleotide Code: Base:...
@m-a-martin ` -b Blank top left corner cell` is about the output cell at (0,0) ?
Until this feature exists, this could work: `seqkit grep -v -f ids_to_ignore.txt < input.afa | snp-dists /dev/stdin > out.tsv`
Normally I would advise running snp-sites -c file.aln | snp-dists /dev/stdin for that case, but it's still worth considering.
This tool was only designed for short reads really - and I hadn't considerd your use case. But you are exactly right! I will have a look at `teloclip` -...
Ah yes, the infamous `X` and `=` operators. I've never seen them used in practice. Do any of the nanopore tools use them? For short reads they would make the...
Best to draw the tree using the MLST allele numbers. With `--legacy --scheme xxx` output it should be easy to put into PhyloViz.
Yes I see your point. I am planning to assign new "IDs" for novel alleles, and use them for all matches in a set if you run `mlst *.fasta` etc....
@Edison2021 i do not understand exactly what you mean? is this different to the existing `--max` option?
So you want the SAM lines where more than 50bp is soft-clipped, or less than 100bp is soft-clipped? Would `samclip --max ?? | samclip -v --max ??` work?