Devon Ryan

samtools isn't using openmp to begin with and I expect a hefty chunk of use is on multi-use clusters that have to patch around buggy behavior in other things (numpy...

Using read names aids reproducibility, or at least I'd think so.

TMPDIR is so widely supported that it would really be nice to not have to manually specify the temporary location in samtools commands (I have users forgetting to do this...

> both represent a separate "reading" of the the base, just like other reads are? They represent separate technical measurements of the same base, but aren't independent since they arise...

UCSC is really annoying since it doesn't have coherent releases (e.g., with a release number). If you know what should be matched together then please submit a PR.

NCBI hosts a file that has a variety of chromosome naming system suggestions, so I use that and compare the chromosome lengths to ensure they match.

Note that there are patch contigs added over time, so these have to be updated every year or two.

Quite likely, yes.

@nh13 Either side-by-side or a subdirectory would work IMO.

Can guppy be redistributed?