New to me #nanopore stuff, sure other folks know this already. If I chop off the first 100 bp from reads, the average quality goes way up. Filtering greater than q20 gave me 20k more reads if I did the chop.

Looking forward to chat at #KidneyWeek @ASNKidney , where we will be showing our pilot work (mostly done by @MorganMacKenz12@twitter.com, I just abused the Xeons for the #bioinformatics) regarding the role of @nanopore #nanopore sequencers in the discovery of kidney disease biomarkers.

Register today for our Nanopore Day in Copenhagen to hear the latest technical updates from Oxford Nanopore Technologies as well as talks from local and international scientists about their work using nanopore technology in human translational and clinical research.

https://nanoporetech.com/nanopore-day-copenhagen-2023

#genomics #clinicalgenomics #nanopore #sequencing

Hey #nanopore users, check out our new application note on using SageHLS for size selection at higher MW cutoff values: https://sagescience.com/application-notes/

Replication is super precise. #methylation #nanopore

"Rapid species discovery and identification with real-time barcoding facilitated by ONTbarcoder 2.0 and Oxford Nanopore R10.4"

https://www.biorxiv.org/content/10.1101/2023.06.26.546538v2

The accompanying video is cool
https://twitter.com/RudolfMeier15/status/1674801657287413760?s=20

#DNAbarcoding #nanopore #GUI

Funny detail found in PubMed searching for "nanopore sequencing": The total number of search results from 2020 equals the ones from 2023 as of today.
The nanopore sequencing technology is currently rising. When will it decline? When every genome of every known species is sequenced, or when another technology outpaces it?
#nanopore #sequencing #pubmed

Funny detail found in PubMed searching for "nanopore sequencing": The total number of search results from 2020 equals the ones from 2023 as of today. The Nanopore sequencing technology is currently rising. When will it decline? When every genome of every known species is sequenced, or when another technology outpaces it?
#nanopore #sequencing #pubmed

@mdperry Hope to integrate those in our pipeline for #nanopore https://www.biorxiv.org/content/10.1101/2022.12.16.520507v1. Just finished rewriting from #Python to #perl and looking for something other than blast (I was unpleasantly surprised by the fragility of kmer seeding methods in the presence of sequencing errors).

Referenced link: https://phys.org/news/2023-06-extreme-dna-resolution-spatially-multiplexed.html
Discuss on https://discu.eu/q/https://phys.org/news/2023-06-extreme-dna-resolution-spatially-multiplexed.html

Originally posted by Phys.org / @physorg_com: http://nitter.platypush.tech/physorg_com/status/1670808664788156417#m

Extreme DNA resolution: Spatially multiplexed single-molecule translocations through a #nanopore at controlled speeds @epfl_en @NatureNano https://phys.org/news/2023-06-extreme-dna-resolution-spatially-multiplexed.html

Anyone have any life changing tips for a first-time #nanopore user? I will be doing some MinION sequencing over the next few weeks.

And this simulation #rstats code, shows why one must use use very short seeds when using #blast to map #nanopore #transcriptomic #RNAseq data (Q10 quality scores are not unheard of, in such datasets).

Take home message, one has got to work for their database searches for long read platforms
(R code in the alt description)

🧐 #MeetTheSpeaker!

🔬 What are the opportunities and the challenges of nanopore sequencing technology? We talked about it with Philipp Rescheneder @nanopore@genomic.social @nanopore@bird.makeup

“One of the things that I like about nanopore sequencing is that it’s very flexible”

#sciencemastodon #science #lifesciences #nanopore #humantechnopole #sequencing

https://www.youtube.com/watch?v=6awqLEHshrY&list=PLZAXXKHOAZejmAUgTARUfsXbREH0qsd9G&index=11

🧐 #MeetTheSpeaker!

🔬 Hazuki Takahashi from RIKEN IMS explains how nanopore long-read #sequencing technology can change research on the #humangenome

https://youtu.be/AzoY5x_hkJs

#sciencemastodon #science #lifesciences #humantechnopole #nanopore @nanopore@genomic.social @nanopore@bird.makeup @riken_en

#Minimap2 #Rust library release: minimap2 v0.1.13+minimap2.2.26

* Latest minimap2 stable release (2.26)
* with_seq function
* hopefully compiles for MacOS / aarch64.
* Still struggling with SSE, I recommend using simde feature
*Soft-clipping properly in CIGAR strings but use caution. Happy to work on it more.

https://github.com/jguhlin/minimap2-rs

https://crates.io/crates/minimap2

And the -sys crate
https://crates.io/crates/minimap2-sys

#bioinformatics #genomics #nanopore #pacbio

Hopefully not taking the server down due to a lack of inodes.... #bioinformatics #genomics #nanopore

Alright, #bioinformatics folk, which multiple sequence #alignment and #clustering packages should I add to my #transcriptomic @nanopore workflow?
Linclust, uclust/ cd-hit are candidates for clustering.
Candidates for MSA: clustal/kalign/hmmalign.
Other suggestions? #nanopore #sequencing

A substantial base calling quality improvement observed beta testing the #nanopore RNA004 direct #rnaseq protocol.
This is empirical data from commercial, multi-tissue RNA after poly(A) selection, aligned to hg38 with miminap2 -a -x splice --secondary=no.
Alignments (especially at splice junctions) look exceptional; I could see potential RNA modifications directly from basecalling output as mutations in IGV

RT @hagentilgner
Andrey & Alla put out the newest version of Isoquant
(https://www.nature.com/articles/s41587-022-01565-y); Results unchanged but memory usage down ~10-15 fold and disk usage down ~5-fold;
https://github.com/ablab/IsoQuant/releases/tag/v3.2.0
#LongRead #RNA @iRnaCosi
#nanopore #pacbio #genomics
#Transcripomics #RNAseq #Splicing

Very cool preprint by Adam P Cribbs's group: "Correcting PCR amplification errors in unique molecular identifiers to generate absolute numbers of sequencing molecules." https://www.biorxiv.org/content/10.1101/2023.04.06.535911v1 with lots of innovative ideas to a) measure and b) correct PCR induced errors in RNA-seq experiments. #rnaseq #ngs #singlecells #compbio #illumina #nanopore