Erik Garrison
MAF is the only creature in the uncanny valley between genome graphs and MSAs. Are there really just a handful of people using MAF? On Fri, Apr 10, 2020, 15:50...
I'm building on Ubuntu 15.04. I assumed it would be linking into the build tree, so this is confusing. I didn't catch any issues with yacc/lex or friends, but maybe...
Any suggestions? Just a word or two about where to hack would speed me on my way to resolve this.
It's funny, I came to ask how strobealign will work with collections of many genomes (we have an immediate application). That would completely not work with this optimization!
For inversion, you need two paths. In the first region of the graph the orientation of the paths is the same. In the inversion region, one path switches orientation and...
How big are your input genomes? If you made one FASTA file from them how big is it? On Thu, Nov 16, 2023, 10:45 Adam Novak ***@***.***> wrote: > I...
An alternative is to map with bwa mem and then use gfainject to get GAF mappings. Then you'll have the reference position for each alignment and it's graph position in...
Did you clone with `git clone --recursive` ? On Tue, Oct 1, 2019 at 1:54 PM Sarah Pohl wrote: > How did you do that? When I try to make...
Why don't you also use vg + strelka? This would confirm if the issue is in the caller or not. On Thu, Jul 30, 2020, 03:00 a00101 wrote: > Thank...
You can do so with --surject-to bam in vg map. On Thu, Jul 30, 2020 at 9:48 AM a00101 wrote: > Thank you for your reply. > > Where Can...