I feel that as nanopore has gotten better the shortcomings of flye have become more obvious.

I would've guessed Alice Roosevelt, but maybe I'm just telling on myself.

You forgot 'sudo'

I'm grateful every day for the opportunity to do fun and interesting work that hopefully helps the people of Alaska.

Yeah, I can see the loophole closures written into that book like battle scars.

I feel like this sort of hobby must have an encyclopedic rule book to prevent shenanigans.

This is really cool, looking forward to checking these out.

He sounds delightful.

Very nice! Looking forward to testing this in the near future.

Most of the samples were at 40-60x, but we had a few between 20-40x that still generated good assemblies. I was using 20x as a floor, but may need to reevaluate that with the current Q scores.

These were clinical isolates grown as pure cultures. RBK114 library, basecalled with sup v5.0, assemble with flye, map with bwa mem, polish with polypolish.

48 samples with single contigs between 1.8 and 2 Mbases at >20x coverage.

18 had 0 changes
15 had 1 change
7 had 2 changes
8 had 3-6 changes

I just ran polypolish on about 50 bacterial genomes(~1.9 megabases each). The vast majority of those assemblies had 0-2 changes.

It's honestly hard to justify running the miseq at this point. Particularly since our wetlab strongly prefers the ONT library prep.

Is there a bluesky version of "I'm in this post and I don't like it"?