Ryan Wick, myself and the team (Louise Judd Tim Stinear Rob Edwards & Sarah) have recently looked at the effect of depth on short-read polishing almost-perfect Nanopore bacterial genomes biorxiv.org/content/10.110… (1/7)

Mandatory reading and surprising results from Michael Hall and colleagues - much better SNP/indel calling results from latest nanopore (beating illumina), and deep learning methods really doing well. Extremely thorough work biorxiv.org/content/10.110…

Excellent talk by George Bouras on short/long/hybrid assembly strategies for optimum chromosome and plasmid assemblies! Loads of information, advice, and great new #bioinformatics tools to use next. #ECCMID24

Is Oxford Nanopore duplex basecalling beneficial for bacterial genome assembly? I did some tests, and it seems like it might be! New blog post here: rrwick.github.io/2024/05/08/dup…

Are you a fan of #klebsiella genomics? Looking for a post-doc role? ...🥁 ... I'm recruiting! Join my team Translational Medicine at Monash University to help us build the first Klebsiella clone risk framework. See details here ⬇️ tinyurl.com/yrka232h Applications close June 9th. DM qs #klebNET Klebsiella Club

I'm recruiting for a new post-doc role based in Melbourne and contributing to #klebNET-GSP activities on #klebsiella genomic surveillance. Sylvain Brisse Kat Holt Centre for Genomic Pathogen Surveillance Chiara Crestani Tom Stanton (he/him) Sophia David Theycallmemaggie Check out the details ⬇️

Our first elife reviewed preprint elifesciences.org/reviewed-prepr…

SPAdes 4.0 is released! github.com/ablab/spades/r… Since 2022 SPAdes is not related to any institution and is maintained by the SPAdes team - an international group of volunteers. Although this might be the last major release, we strongly intend to continue supporting our users!

The final version of our short-read polishing manuscript (headed by Ryan Wick of course) is out in Microbiology Society MGen! Tldr: with R10.4.1+Dorado ONT assemblies, few errors remain, so short-read polishing can make assemblies worse at low depth; target >=25x doi.org/10.1099/mgen.0…

I am excited to win a CZI EOSS grant! This is the first grant I have ever won after 20+ years in science. It feels wonderful to finally be funded for my open-source contributions. With Wytamma we will deliver the next generation of my popular Snippy software! 🦘🦘🦘

It has been public for a while, but with #VoM2024 starting, today is as good as any to introduce our new tool phage genome annotation tool Phold. Phold uses structural homology to assign functions to phage proteins (1/n)

How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies. Published #OpenAccess and fee-free in #MGen using a #PublishAndRead agreement: doi.org/10.1099/mgen.0…

I finally got around to testing HERRO (github.com/lbcb-sci/herro), the new Oxford Nanopore read correction algorithm which takes simplex ONT reads to PacBio-HiFi-level accuracy. I was impressed! Findings are on my blog in a two-part post: rrwick.github.io/2024/07/26/her… rrwick.github.io/2024/07/31/her…

Our OnION sequencing computer now has a little sibling: Spring OnION! Short post with some stats and benchmarks: rrwick.github.io/2024/08/16/spr…