Yusuke Okazaki
@yusukeokazaki.bsky.social
📤 17
đź“Ą 28
đź“ť 2
Working on aquatic microbial ecology in Japan.
https://yusukeokazaki.weebly.com/
reposted by
Yusuke Okazaki
SAME18-BCN
3 months ago
Group pic SAME18!
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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...
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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
https://academic.oup.com/ismecommun/advance-article/doi/10.1093/ismeco/ycaf086/8139868
7 months ago
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reposted by
Yusuke Okazaki
George Bouras
7 months ago
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...
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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 ...
https://www.biorxiv.org/content/10.1101/2025.05.12.653612v1
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reposted by
Yusuke Okazaki
SAME18-BCN
9 months ago
🌊 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
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Microbiome Notes—Building a Library of Descriptive Microbial Ecology
enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
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Microbiome Notes—Building a Library of Descriptive Microbial Ecology
Click on the article title to read more.
https://enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/1758-2229.70085
9 months ago
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reposted by
Yusuke Okazaki
Ryan Wick
10 months ago
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)
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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...
https://www.biorxiv.org/content/10.1101/2025.02.20.639404v1
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