David Eccles 🌻🇵🇸6x🩹🛡️@nanopore Updated: GPU/MinKNOW basecalling server walkthrough:
https://gringer.gitlab.io/presentation-notes/2021/10/08/gpu-calling-in-minknow/
GenomiqueENS📣 Que quelques places ! 4 sessions de formation destinées aux personnes disposant ou souhaitant acquérir un séquenceur
#OxfordNanopore #MinION ou #P2solo : 📷 4 avril, 27 mai (expériences) 📷 5 avril, 28 mai (bioinfo). Conseil : n'attendez pas😉
👉 https://genomique.biologie.ens.fr/fr/actualites_et_publications/emplois_et_formations
@nanopore We're running another lot of cDNA samples on our P2 Solo. Flow cell loading and available pores looks great. Not quite a full sea of green, but that's to be expected from an older PromethION flow cell. They seem to be more time-sensitive than the MinION and Flongle flow cells.
@nanopore Super-accuracy basecalling is done for our most recent P2 Solo runs. I'm seeing about q20 modal accuracy from mapped reads.
@nanopore we actually crossed over 70M reads with one of the flow cells!
@nanopore I now have a comparison of the same sample on Flongle (cleanup using SFB) and PromethION (cleanup using LFB) flow cells.
These were both called with the new bacterial caller in simplex mode. According to LAST-train, the qScore-adjusted substitution accuracy for the Flongle was q41, and the qScore-adjusted substitution accuracy for the PromethION was q45.
@nanopore hmm... looks like I messed up on the 3kb and 1.5kb ladder bands.
This new kmer-based mapper seems to be doing the right things, though. I'm very pleased.
@[email protected] That new bacterial @nanopore bascalling model is doing pretty well.
#P2Solo Data upload to our experimental archive. 641.15 GB of raw pod5 files. This was the lower end of acceptable data output for a P2 Solo run (about 50 Gb of sequence data).
@nanopore #P2Solo another cDNA run that has exceeded 25M reads. The computer froze [again] in the middle of a sequencing run, after getting 6.24M reads, but I now have >25M reads from after the restart.
[FWIW, I care about 25M because that's the maximum that could ever be generated from a single Revio run, assuming perfect performance from all ZMWs]