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long read assemblers that are amenable for use with Oxford Nanopore data? My list right now is goldrush, verkko, canu, flye, nextdenovo, hifiasm, raven, shasta (previously mecat and miniasm but those are slightly out of date).

Have you ever read a paper (or seen a talk) where you feel the author is reading your mind? Like any concern is immediately addressed right after it crosses your mind? I think that is a hallmark of great writing, and I have a theory about it. A thread... 1/12

Had a quick bacterial Oxford Nanopore assembly tutorial yesterday with a colleague and made a short summary. Not as useful as Ryan Wick spectacular repo github.com/rrwick/Perfect… but maybe good if you want assembly fast (~15 min) and are command line proficient. github.com/osilander/simp…

this is a great comparison of fastq compression with gz and zstd, both ONT and Illumina data github.com/mbhall88/compr…

So excited to announce that m6anet now supports the new RNA004 chemistry from Oxford Nanopore!! github.com/GoekeLab/m6anet 1/4

Do people ever bootstrap taxa instead of alignment columns to measure phylogenetic certainty/uncertainty? Or is this silly/impossible?

⚠️ It is unfortunately that time again and my current work contract is ending soon. If anyone has a microbial #genomics #postdoc or scientific job opening (service, research, teaching & communications positions will all be considered), hire me! linkedin.com/in/melinda-ash…

Hi guys, SeqKit v2.5.1 fixed a concurrency bug (file name error) introduced in v2.5.0, please update. github.com/shenwei356/seq…

🔥 Bactopia v3 is here! 🔥 The Nextflow pipeline for bacterial genomes is now faster, packed with more tools, updated docs, and much much more! Get started at: bactopia.github.io/v3.0.0/ #bioinformatics #genomics

CATASTROPHIC LOSSES TO NATURAL SCIENCES, FOOD TECH AND ENGINEERING AT Massey University PROPOSED TODAY. 60% of staff to go across these areas. Shut down of these capabilities at Albany. Engineering cut altogether. Plant science also cut. Massey: taking the 'Universal' out of University.

Troy Baisden 🌏 💦 🌱🌻 Richard Easther David Eccles 🌻🇵🇸6x🩹🛡️ @Jamienzherald It is the staff who occupy this building Massey University whom are being made redundant (Ecology, Molecular Bio, Chemistry, Food tech, etc). The space was purpose-built for them, opened in Feb this year. So many talented staff are being fired; terminating many postgrad projects.

Dorado v0.4.0 is live! - barcode demux & trimming - simplex read splitting - improved 6mA, 5mC/5hmC GpG models - new 5mC/5hmC all context model - increasing duplex pairing rates Plus a whole bunch more.. github.com/nanoporetech/d…

New blog post: rrwick.github.io/2023/11/06/acc… I took the ONT data from my last post, subsampled to various depths and assembled with Flye. Reveals what ONT-only accuracy looks like with a 'normal' read depth and Flye assembly (as opposed to extra-deep reads and Trycycler assembly).

A High-quality Oxford Nanopore Assembly of the Hourglass Dolphin (Sagmatias cruciger) Genome dlvr.it/T7lfBf