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rrwick.bsky.social
Bioinformatician at the Centre for Pathogen Genomics at the University of Melbourne
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A new long-read metagenome assembler has been released: myloasm. Very exciting! Looking forward to trying it out.

submitted 8 days ago • 1 comment

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

submitted 8 days ago • 5 comments

New blog post! In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup. Check it out for the full results: rrwick.github.io/2025/05/27/d...

submitted 10 days ago • 4 comments

New version of Dorado is out: github.com/nanoporetech... And for the first time in a year, this includes new DNA basecalling models! I'll try out these new models (v5.2.0) and compare them to the previous ones (v5.0.0) in a blog post in the near future.

submitted 15 days ago • 0 comments

New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention). www.biorxiv.org/content/10.1... (1/6)

submitted 16 days ago • 1 comment

Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well www.biorxiv.org/content/10.1...

submitted 18 days ago • 4 comments

Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them? If so, you might this little project: github.com/rrwick/conda...

submitted 71 days ago • 1 comment

New preprint is out! We investigate how well you can call variants directly from genome assemblies compared to traditional read-based variant calling. Read it here: www.biorxiv.org/content/10.1... Data & code: github.com/rrwick/Are-r... (1/8)

submitted 95 days ago • 2 comments

I re-ran previous ONT basecalling benchmarks using the latest version of Dorado (thanks, @vellamike.bsky.social), and the RTX 40 series GPUs show an impressive speed boost! Check out the updated benchmark results at the bottom of this post: rrwick.github.io/2024/08/16/s...

submitted 105 days ago • 0 comments

Dorado now supports bacterial genome polishing. It can output assemblies in FASTQ, including Q scores. @rrwick.bsky.social 's analysis shows Q scores are well correlated with base call reliability, meaning they can help reduce false positives in variant calling. rrwick.github.io/2025/02/19/f...

submitted 106 days ago • 0 comments

A quick reminder: if CheckM reports an assembly as <100% complete and >0% contaminated, that doesn't necessarily mean it's incomplete or contaminated. Here are RefSeq's CheckM results for a genome I'm confident is 100% complete and 0% contaminated.

submitted 106 days ago • 6 comments

New blog post! Ever seen a genome assembly in FASTQ format instead of FASTA? Dorado polish from @nanoporetech.com can do it, and I took a closer look: rrwick.github.io/2025/02/19/f...

submitted 107 days ago • 1 comment

Dorado v0.9.1 now includes a bacterial model for genome polishing, so I put it to the test! How does it compare to Medaka? And does move-table data improve polishing accuracy? Read my analysis here: rrwick.github.io/2025/02/07/d...

submitted 119 days ago • 2 comments

Do you make core genome alignments for phylogenomics? Mona Taouk and I explored how including sites with some missing data (a soft core) can improve analysis, especially for large datasets. www.microbiologyresearch.org/content/jour... (1/4)

submitted 136 days ago • 2 comments