I have distracted myself this week with the extraordinarily mundane task of designing a sample identifier scheme. I want to share some decisions I made in the hope that it saves somebody else some time. The first choice was the alphabet. I wanted to use human friendly, familiar ASCII characters, but intentionally leave out potentially confusing characters. I'd previously read about "Crockford's base32" (crockford.com/base32.html) which tries to address this problem.

Something I briefly mentioned in my talk but forgot to emphasise on in the panel was that "real bioinformatics" is not just writing the fanciest aligner or assembler. We really do need to invest time and people in hooking these tools together in a way that is robust and accurate!

https://twitter.com/kirk3gaard/status/1273577318544486401

Every new tool is part of an ecosystem. You may have the most accurate assembler, but maybe it doesn't work well with downstream tools. Maybe your aligner gives funky results with a certain basecaller. We should develop tools in conjunction with how we think they will get used.

idk who this @pathogenomenick guy is but he seems like a big deal Here early to get a seat for Nick's inaugural lecture at @unibirmingham @IMIBirmingham. The Dome theatre is living up to its name.

In the #nanoporeconf data theatre with @Scalene talking about our recent Gigascience paper on sequencing the Zymo mock community, and his new DNA extraction method academic.oup.com/gigascience/ar… Introducing the "three peaks challenge", three DNA extractions to ensure representation. "it's not ok to sacrifice representation to get long reads"

Our paper: "Ultra-deep, long-read nanopore sequencing of mock microbial community standards", is out today! Featuring some seriously juicy @nanopore sequencing from @Scalene, and some cool assembly and analyses from me and @pathogenomenick.
academic.oup.com/gigascience/ar… We had a Q&A about our work with editor @SCEdmunds, talking mock metagenomes and breaking the first rule of @longreadclub gigasciencejournal.com/blog/mock-meta…
And now, a thread:

Pumping myself full of coffee this morning to prepare for a @nanopore workshop on applying CUDA to bioinformatics, or as I explained to my sister "using computer graphics cards to science more fast" Things are looking up after yesterday's disasters. I've made it to the venue and it's quite fancy.