Senior Research Fellow, Liggins Institute, University of Auckland, Tāmaki Makaurau, Aotearoa. Evolutionary biologist and wannabe microbiologist. he/him.
Auckland, Aotearoa
Joined March 2010
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Our paper on the evolution of gene regulation was published today bitly.ws/td4G. Years of hard work and hard thinking by @m_vlkova. I really like this paper. (1/8)
Olin Silander retweeted
A High-quality Oxford Nanopore Assembly of the Hourglass Dolphin (Sagmatias cruciger) Genome dlvr.it/T7lfBf
The disestablishment will disrupt or even destroy the trajectory of many people's careers. Not sure what else to say.
Olin Silander retweeted
New blog post: rrwick.github.io/2023/11/06/…
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).
Olin Silander retweeted
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/dora…
Olin Silander retweeted
It is the staff who occupy this building @masseyUni 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.
Olin Silander retweeted
CATASTROPHIC LOSSES TO NATURAL SCIENCES, FOOD TECH AND ENGINEERING AT @MasseyUni 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.
Olin Silander retweeted
🔥 Bactopia v3 is here! 🔥
The @nextflowio 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
Olin Silander retweeted
Hi guys, SeqKit v2.5.1 fixed a concurrency bug (file name error) introduced in v2.5.0, please update.
github.com/shenwei356/seqkit…
Olin Silander retweeted
⚠️ 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-ashc…
Do people ever bootstrap taxa instead of alignment columns to measure phylogenetic certainty/uncertainty? Or is this silly/impossible?
Olin Silander retweeted
So excited to announce that m6anet now supports the new RNA004 chemistry from @nanopore!!
github.com/GoekeLab/m6anet
1/4
this is a great comparison of fastq compression with gz and zstd, both ONT and Illumina data github.com/mbhall88/compress…
Had a quick bacterial @nanopore assembly tutorial yesterday with a colleague and made a short summary. Not as useful as @rrwick spectacular repo github.com/rrwick/Perfect-ba… but maybe good if you want assembly fast (~15 min) and are command line proficient. github.com/osilander/simple-…
Olin Silander retweeted
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
long read assemblers that are amenable for use with @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).