Pinned Tweet
This will be my last post here. I'm moving to Bluesky:
bsky.app/profile/rrwick…
Hope to see you there!
bsky.app/profile/rrwick…
Hope to see you there!
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Do you make core genome alignments for phylogenomics? @monaltaouk and I explored how including sites with some missing data (a soft core) can improve analysis, especially for large datasets.
microbiologyresearch.org/content/journa…
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microbiologyresearch.org/content/journa…
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And the benefits grow with dataset size! A 100% strict core may work fine for small datasets (e.g. ~10 genomes) but is devastating for very large ones (e.g. 1000+ genomes). A 95% soft core works well across all dataset sizes.
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To make producing soft core alignments easier, we developed Core-SNP-filter, a simple and efficient tool to process SNP alignments with user-defined thresholds.
github.com/rrwick/Core-SN…
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github.com/rrwick/Core-SN…
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New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autocyc…
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I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autocyc…
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However, Autocycler still allows users to manually intervene when they would like to. So it aims for the best of both worlds: either hands-off automated assemblies or hands-on curated assemblies, as the user sees fit.
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Autocycler is still new and evolving. I'll continue to improve it based on your feedback. A big thank you to the alpha testers who gave me feedback before this release! Give it a try and share your thoughts.
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Just had my first experience with CycloneSEQ data and shared my findings in this blog post:
rrwick.github.io/2024/12/17/cyc…
How does CycloneSEQ compare to @nanopore? I looked at both read-level and consensus-level accuracy. Check it out!
rrwick.github.io/2024/12/17/cyc…
How does CycloneSEQ compare to @nanopore? I looked at both read-level and consensus-level accuracy. Check it out!
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Ryan Wick retweeted
If you want to try out the new --bacteria Medaka polishing option after reading Ryan's thoughts in his latest blogpost, the newest Hybacter v0.10.0 release now includes it as the default
github.com/gbouras13/hybr…
github.com/gbouras13/hybr…
A little bit overdue, but here are my thoughts on @nanopore's recent release of Medaka:
rrwick.github.io/2024/10/17/med…
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A little bit overdue, but here are my thoughts on @nanopore's recent release of Medaka:
rrwick.github.io/2024/10/17/med…
rrwick.github.io/2024/10/17/med…
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Ryan Wick retweeted
Excited to share this preprint where we’ve used genomic analysis of >3000 genomes to study Klebsiella pneumoniae in a One Health perspective 🦠🔬👩💻#OneHealth #KLEBGAP #KlebClub @IrenLohr @DrKatHolt @NORKLEBNET
A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events ... biorxiv.org/cgi/content/sh… #biorxiv_micrbio
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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…
Short post with some stats and benchmarks: rrwick.github.io/2024/08/16/spr…
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I finally got around to testing HERRO (github.com/lbcb-sci/herro), the new @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…
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…
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Ryan Wick retweeted
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…
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Ryan Wick retweeted
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)
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Ryan Wick retweeted
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! 🦘🦘🦘
Open source tools are crucial for biomedical research. We're collaborating with @KavliFoundation + @wellcometrust to support developers & maintainers of critical #OpenSource projects, promoting innovation & community engagement in the field. More ▶️ czi.co/3zjN56l
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New blog post:
rrwick.github.io/2024/06/11/sho…
ONT-only bacterial assemblies are much better than they were only a couple of years ago. Often <10 errors in the whole genome. Does that mean that less short-read sequencing is required for polishing? See my post for the answer!
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rrwick.github.io/2024/06/11/sho…
ONT-only bacterial assemblies are much better than they were only a couple of years ago. Often <10 errors in the whole genome. Does that mean that less short-read sequencing is required for polishing? See my post for the answer!
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The paper also introduces George's tool Pypolca:
github.com/gbouras13/pypo…
This is a reimplementation of the POLCA polisher (by @AlekseyZimin5) that is easier to install and run. Pypolca also has some new options (e.g. --careful) which give it more flexibility than POLCA.
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github.com/gbouras13/pypo…
This is a reimplementation of the POLCA polisher (by @AlekseyZimin5) that is easier to install and run. Pypolca also has some new options (e.g. --careful) which give it more flexibility than POLCA.
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