Yusuke Okazaki

Group pic SAME18!

Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus–host pairing of freshwater bacteria Abstract. Characterizing virus–host pairs and the infection state of individual cells is the major technical challenge in microbial ecology. We addressed t

Our new paper comes out! Single-cell genomics linked many freshwater virus-host pairs and identified wanted CL500-11 viruses. The varying infection rates among host lineages highlighted their diverse defense strategies depending on their ecological characteristics: academic.oup.com/ismecommun/a...

Autocycler: long-read consensus assembly for bacterial genomes Motivation: Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using ...

www.biorxiv.org/content/10.1...

Autocycler, the automated successor to Trycycler from @rrwick.bsky.social has a pre-print out - overall, pretty awesome performance (and is very easy to use)

github.com/rrwick/Autoc...

🌊 Save the Date! 🌍
#SAME18 — Aquatic Microbiomes on a Changing Planet
📍 Barcelona, Spain | 🗓️ Sept 28 – Oct 3, 2025
At the iconic PRBB 🧬🌿
Join us to explore the frontiers of aquatic microbial ecology.

📢 Stay tuned for more info and follow us on Bluesky!

#MicrobialEcology #MarineMicrobiology #SAME18

Microbiome Notes—Building a Library of Descriptive Microbial Ecology Click on the article title to read more.

Microbiome Notes—Building a Library of Descriptive Microbial Ecology enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

Are reads required? High-precision variant calling from bacterial genome assemblies Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared...

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...
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