Robert Edgar

No errors or warnings AFAICS when -`v 0` is removed. I posted files with a `runme.bash` here: [https://drive5.com/tmp/for_milot.tar.gz](https://drive5.com/tmp/for_milot.tar.gz)

Great feedback, thanks! Yes, the sequences are highly diverged; I'm attempting to align many pairs of MSAs where the sequences are diverged to something like 5 substitutions per site. However,...

"all coding regions (showing start and stop codons, if present)" Finding start and stop codons is difficult with Cov, this is the main reason I gave up trying to do...

Figuring out CDS and gene symbols is also tricky because of the polyprotein which is cleaved into multiple genes. In these cases, both the poloyprotein before cleavage and the genes...

Here is a nice figure showing the complexity of an example Cov genome (SARS-CoV-1). Note the multiple levels of overlapping and nested ORFs and CDSs with a frameshift in one...

Is cleavage well enough understood to know how well conserved the sites are, or if approximate sequence conservation necessarily implies cleavage or not? If the genome is diverged 1%, 2%,...

Sure, I saw the screenshots and it looks like the best-known genes are in roughly the right place, but I don't know if GenBank will find this acceptable. I don't...

@taltman Can you point me at the relevant documentation? As I understand it, the Kraken2 index doesn't store coordinates of k-mers, only taxonomy ids, so this would need to be...

@ababaian As I understand it, that figure was made by the sliding window method followed by manual (i.e. visual) analysis to identify the discontinuities. That's fine for a single genome,...

Yes, exactly -- the question was whether we/I need to write a new tool for this. If someone else would like to tackle this one, great!