Fredrik Dyrkell

Control Structures, English translation of @cdf1530 lectures by Xavier Leroy discuss.ocaml.org/t/control-stru…

It's time to donate #usearch to the scientific community, with many sincere thanks to users who supported this research through license fees.

Presenting sylph (github.com/bluenote-1577/…), a fast, precise metagenomic profiler. Work done with @YunWilliamYu. sylph is highly accurate at the species level and takes ~1 minute and 16 GB RAM to profile against 85k prokaryotes and 2.9 million viral genomes. 1/10

Amazing story about a rubik cube themed jigsaw puzzle and a solver written in Zig, with a dash of @raylibtech for visual feedback. zig.news/shadeops/zig-a…

Hey @phrenopolis, Guybrush invited us to meet him at the Scumm Bar this evening. You coming? I'm going to show up fashionably late. #MonkeyIslandMonday #ReturnToMonkeyIsland

Our long read mapping survey is now on bioRxiv 🎉

@BQPMalfoy Both SKESA and IDBA-UD can generate GFA graphs but with additional tools. SKESA includes in the repo, and for IDBA I have used this: github.com/rrwick/IDBA-to…

Is there any short read assembler that generate contigs in GFA format ? (Besides the invaluable SPAdes assembler)

@docpolski Thanks for the recommendation Paul, hoping to join 👍

Kit14 coming up @nanopore faster and better accuracy 🎉

@Johngorzynski, @kishwarshafin and I are excited to present the details of our ultra-rapid @nanopore whole genome sequencing pipeline (nejm.org/doi/full/10.10……) published in @NatureBiotech nature.com/articles/s4158… today! The pipeline produces a genetic diagnosis in under 8 hrs.

Picking read size and running adaptive sampling directly in @nanopore minknow is now available 🎉😁 #SQK-NBD112-24 prep of pure cultures. Looking forward to a RBK version for faster prep.

New paper led by @mbhall88 and collaborators! Evaluating @nanopore as a replacement/complement for Illumina for TB: drug resistance and clustering. Spoiler: you can get equivalent clustering and identical resistant predictions (with 30x depth). 1/n medrxiv.org/content/10.110…

'The Fly' My latest #GLSL #shader scene written with #Shadertoy. Source: shadertoy.com/view/ft2XWw No 3D models. No textures. 100% code. #realtimeVFX

Wonderful ->

Yet another genome assembler, this time it is written in Rust. Peregrine-2021: A faster and minimum genome assembler for long-reads with good enough accuracy github.com/cschin/peregri… #genomics #bioinformatics #rustlang

Control Group xkcd.com/2576

Very happy to have my first paper published as part of my PhD, "Optimising genomic approaches for identifying VRE transmission in healthcare settings". Thanks to all involved for their help along the way. nature.com/articles/s4146…

So for most modern hybrid read-sets, I'd recommend a long-read-first assembly approach: assemble the long reads and use short reads only for final polishing. I've made Trycycler and Polypolish to help with this: github.com/rrwick/Trycycl… github.com/rrwick/Polypol… (6/8)

Peter Norvig’s Python etudes github.com/norvig/pytudes