mcfrith

1- Each read is simply assigned to the allele with nearest copy-number-change (breaking ties by choosing the shorter allele). The `-v` output shows each read's copy-number-change. 2- You can do...

The "consensus" should be robust to "outliers"... but only up to a point.

Many thanks for your interest in tandem-genotypes. What you're doing seems correct: I don't know why it doesn't work. Maybe if you could share your intermediate files... To know which...

Thanks for this interesting example! In short, tandem-genotypes is "working as designed", but the design isn't looking good in this case. It's faithfully following the "tandem-genotypes method" in here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1667-6...

Unfortunately `last` does not (yet) have such a mode. Maybe one day, but probably not in the near future. Naive self-alignment with `last` is not catastrophically inefficient, at least. I'll...

My best guess is: `$denovo_assembly` doesn't have the right file name, or something like that. Indeed your sequence format looks fine, yet `Query sequences=0`: impossible!

Hi, I copy-pasted your 3 sequences and lastal options. I got the expected `Query sequences=3`. Could you send some minimal sequence files and exact options (including for lastdb) that exhibit...

Apparently, you can attach files to these comments: https://docs.github.com/en/free-pro-team@latest/github/managing-your-work-on-github/file-attachments-on-issues-and-pull-requests Or you could email them to my address shown in here: https://sites.google.com/site/mcfrith/

Hi: I tried your commands and sequences, with LAST version 1060, and got the expected `# Query sequences=1558`. (I don't have `Termitomyces_v3.0.fa`, so I used some random file instead, but...

Please can you show your commands/options for `lastdb` and `last-train`, and also the version (e.g. `lastdb --version`)?