Georges Kanaan

@ivagljiva would you rather see an implementation like what was [done](https://github.com/merenlab/anvio/pull/2244) for the MDM Defense Finder HMMs with an `anvi-script-gen-phrogs-hmm-directory` command, or something more integrated such as `anvi-run-phrogs`? I guess...

I could also look at this after ISME if no-one else does.

Seems like people have already contributed this to bioconda: [anvio](https://github.com/bioconda/bioconda-recipes/blob/master/recipes/anvio/meta.yaml) and [anvio-minimal](https://github.com/bioconda/bioconda-recipes/blob/master/recipes/anvio-minimal/meta.yaml). Someone in the merenlab could be marked as maintainer and the future work would just need to keep...

@ArtRand, another suggestion would be to clarify the docs to state whether the positions printed are for the first nucleotide of the motif or the methylated nucleotide. I believe it's...

I wanted to chime in here in support of this command. I have explored many different methods for quantifying how differently methylated a nucleotide is in different samples. I've typically...

Looking at this after posting it, could it be this is just because the coverage is too low? Does that track with the error being printed? I read it as...

@ArtRand would it be useful for me to share this with you, do you happen to have an FTP server set up by any chance? I can try to truncate...

Got it, I think that's likely the issue. Any chance we could have that output a different error message when coverage is the restriction filtering out bases? Rather than an...

@wdecoster seems like NanoComp only supports aligned BAM files however, what would be the logical way to use it with the unaligned barcodes given by dorado? Also what is the...

Yeah multivariate may be complicated, though perhaps you could do multiple parities tests? If any are different then it is surely different, if all are the same then they are...