Yusuke Okazaki
@yusukeokazaki.bsky.social
Working on aquatic microbial ecology in Japan. https://yusukeokazaki.weebly.com/
Reposted by Yusuke Okazaki
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...
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
academic.oup.com
May 21, 2025 at 2:13 PM
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...
Reposted by Yusuke Okazaki
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...
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...
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
May 16, 2025 at 12:22 AM
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...
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...
Reposted by Yusuke Okazaki
🌊 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
#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
March 22, 2025 at 12:47 PM
🌊 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
#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 enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
Microbiome Notes—Building a Library of Descriptive Microbial Ecology
Click on the article title to read more.
enviromicro-journals.onlinelibrary.wiley.com
March 28, 2025 at 12:48 PM
Microbiome Notes—Building a Library of Descriptive Microbial Ecology enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Yusuke Okazaki
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)
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)
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...
www.biorxiv.org
March 3, 2025 at 3:24 AM
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)
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)