SEA-PHAGES | All posts created by plyp

Link to this post \| posted 07 Nov, 2025 20:46
plyp	Hi all, I had mentioned at the 2024 Faculty meeting that we were optimizing our Nanopore workflow to work with DNA from a single plaque pick bypasssing the need for webbed plates, passaging or even DNA extractions. Many of you had expressed interest in the technique and I promised to follow up once it was reliable. I wasn’t able to attend the inaugural bacteriophage conference but I’m happy to announce our preprint detailing our methods for one day genomes from single plaques, with a former SEA-PHAGES student as first author! https://www.biorxiv.org/content/10.1101/2025.10.21.683754v1 Happy readings, Patrick

Link to this post | posted 07 Nov, 2025 20:46

Hi all,
I had mentioned at the 2024 Faculty meeting that we were optimizing our Nanopore workflow to work with DNA from a single plaque pick bypasssing the need for webbed plates, passaging or even DNA extractions. Many of you had expressed interest in the technique and I promised to follow up once it was reliable.

I wasn’t able to attend the inaugural bacteriophage conference but I’m happy to announce our preprint detailing our methods for one day genomes from single plaques, with a former SEA-PHAGES student as first author!

https://www.biorxiv.org/content/10.1101/2025.10.21.683754v1
Happy readings,
Patrick

Posted in: General Message Board → Single plaque Nanopore sequencing

Link to this post \| posted 02 Jan, 2024 19:41
plyp	Hello all, We've had issues with running a full VM with some laptops that are near full or shipped with the lowest storage tiers and can't afford to run an entire virtual machine plus windows just for one software. I found and tested a new app called Whisky that's extremely simple to use and very lightweight. I haven't found any real bugs so far (I get a glimmer error at this moment but the glimmer calls are still being made, it seems to be more related to gene mark and the exact same error is currently happening on real windows machines) The Whisky application can be downloaded from: https://getwhisky.app/ Tested confirmed features: • Preferences are saved between launches • Auto update to 2705 • Gene starts called the same way • BLAST connections work • Fasta/dnam5 files can be easily saved and are accessible directly through Finder for sharing (Open C: drive on startup screen) • Maximum RAM usage at 900MB, Maximum disk usage below 1.4GB Im attaching a quick guide with screenshot instructions Patrick Łypaczewski 2.72Mb

Link to this post | posted 02 Jan, 2024 19:41

plyp

Hello all,
We've had issues with running a full VM with some laptops that are near full or shipped with the lowest storage tiers and can't afford to run an entire virtual machine plus windows just for one software. I found and tested a new app called Whisky that's extremely simple to use and very lightweight. I haven't found any real bugs so far (I get a glimmer error at this moment but the glimmer calls are still being made, it seems to be more related to gene mark and the exact same error is currently happening on real windows machines)
The Whisky application can be downloaded from:
https://getwhisky.app/

Tested confirmed features:
• Preferences are saved between launches
• Auto update to 2705
• Gene starts called the same way
• BLAST connections work
• Fasta/dnam5 files can be easily saved and are accessible directly through Finder for sharing (Open C: drive on startup screen)
• Maximum RAM usage at 900MB, Maximum disk usage below 1.4GB
Im attaching a quick guide with screenshot instructions

Patrick Łypaczewski

Posted in: DNA Master → DNA Master on M1 Mac

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