naturepoker

Catching up on some personal #prophage work. Couple of tooling changes worth noting.

1> Genomad is noticeably faster at bulk processing compared to other comparable pipelines. If you haven't already you should really try it out

2> Latest Phold gpu performance feels a LOT faster and lighter

#bioinformatics #microbiology

Feb 4 at 11:28pmWeb
Show threadAdam RetchlessFeb 5
@naturepoker I'm guessing you mean geNomad (which identifies viruses and plasmids) and not genomAD (which does some other genome stuff).
I agree that geNomad is a handy tool.
https://github.com/apcamargo/genomad
GitHub - apcamargo/genomad: geNomad: Identification of mobile genetic elements

geNomad: Identification of mobile genetic elements - apcamargo/genomad

GitHub
Show threadnaturepokerFeb 5

@adamr oh yeah. Hope the lack of proper capitalization won't confuse folks!

I was mostly using virsorter2 as part of an internal pipeline until recently, genomad just seems to work better in most scenarios

Show threadAdam RetchlessFeb 5
@naturepoker yeah, genomAD probably does something completely different. I've never looked into it, I just get frustrated because usually it's enough to add "bioinformatics" to a web search when I want the website for some bioinformatics tool... but it doesn't work here.