Erik Garrison

The remote system is a debian one in [octopus](https://github.com/genenetwork/gn-docs/blob/master/general/help/facilities.md#octopus-hpc-cluster), while the local one is a Ryzen laptop. So they have in common the fact that they are recent AMD systems....

>> Non-GAM textual output (GAF?) to simplify downstream processing of alignments > This sounds totally reasonable. I saw you just released this. Nice! You're the second implementation. I'll add output...

That works, but encourages information loss and ambiguity. I would prefer that SVs that are discovered directly by alignment should be described in a single line. A whole genome aligner...

We have a guix package model to build it. I think it is in my guix-genomics repo. On Mon, Mar 23, 2020, 19:21 Ryan Lorig-Roach wrote: > Building independently from...

Why not use the GFA from pggb directy? On Thu, Dec 3, 2020 at 2:40 AM XuewenWangUGA wrote: > I have a genome graph generated from pggb and then convert...

vg should be able to, but I'm not sure if it's been tested. @glennhickey ? On Thu, Dec 3, 2020 at 4:30 PM XuewenWangUGA wrote: > Erik, > > I...

It's OK if things split. That's at least supported pretty well in the GAM format. The path of such an alignment isn't necessarily in the graph. vg will do the...

vg does do the splitting, but it's slow. (Rather than try to improve it's behavior for long reads, I'm inclined to develop a new aligner.) What's needed here is a...

> I don't like the idea of using a filter based on the cigar string because it is not always present in all files. But this is not a fundamental...

I just got a failed build involving ncurses. Seems it's necessary to install c2hs (`apt install c2hs` on ubuntu/debian).