Wytamma
@wytamma.bsky.social
Enjoying the little things like antibodies, ion channels and pip installs - technical biologist building tools and studying diseases ❤️🐢
Reposted by Wytamma
Wytamma Wirth from @thedohertyinst.bsky.social speaking about a new deep learning approach to bacterial taxonomic classification
November 14, 2025 at 1:38 AM
Wytamma Wirth from @thedohertyinst.bsky.social speaking about a new deep learning approach to bacterial taxonomic classification
Sci-nonfi
October 24, 2025 at 9:27 PM
Sci-nonfi
Reposted by Wytamma
Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
October 9, 2025 at 5:05 PM
Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
Great work team!!
Until next year, @mozztacular.bsky.social, Asad, @royalfizzbin.bsky.social, Mozammel, @wytamma.bsky.social , Bec, and @rhyshparry.bsky.social out!
#MicroSeq2025
#MicroSeq2025
September 4, 2025 at 11:28 PM
Great work team!!
Reposted by Wytamma
Your #MicroSeq2025 committee - @mozztacular.bsky.social , Asad Prodhan, @royalfizzbin.bsky.social , Mozammel Hoque, @wytamma.bsky.social , Rebecca Roach, and @rhyshparry.bsky.social - are all here and ready to go! 🫡
Please feel free to reach out to any of us w/ questions or concerns at any time ♥️
Please feel free to reach out to any of us w/ questions or concerns at any time ♥️
September 3, 2025 at 12:31 AM
Your #MicroSeq2025 committee - @mozztacular.bsky.social , Asad Prodhan, @royalfizzbin.bsky.social , Mozammel Hoque, @wytamma.bsky.social , Rebecca Roach, and @rhyshparry.bsky.social - are all here and ready to go! 🫡
Please feel free to reach out to any of us w/ questions or concerns at any time ♥️
Please feel free to reach out to any of us w/ questions or concerns at any time ♥️
Reposted by Wytamma
Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Protein Structure Informed Bacteriophage Genome Annotation with Phold
Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...
www.biorxiv.org
August 8, 2025 at 7:11 AM
Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Wytamma
Howdy! I'm currently writing up version 4 of Bactopia!
Similar to previous major versions, I've started an issue on Github to track v4 progress. If you are a user of Bactopia and would like to help with feedback or with code, check out the following link:
github.com/bactopia/bac...
Similar to previous major versions, I've started an issue on Github to track v4 progress. If you are a user of Bactopia and would like to help with feedback or with code, check out the following link:
github.com/bactopia/bac...
Bactopia v4 - Overview & Help Wanted · Issue #628 · bactopia/bactopia
Bactopia v4 Yo! Well, it is about that time! I am planning to release version 4 of Bactopia in the near future. With this version, Bactopia will introduce new and exciting things, but at the same t...
github.com
August 6, 2025 at 8:20 PM
Howdy! I'm currently writing up version 4 of Bactopia!
Similar to previous major versions, I've started an issue on Github to track v4 progress. If you are a user of Bactopia and would like to help with feedback or with code, check out the following link:
github.com/bactopia/bac...
Similar to previous major versions, I've started an issue on Github to track v4 progress. If you are a user of Bactopia and would like to help with feedback or with code, check out the following link:
github.com/bactopia/bac...
Reposted by Wytamma
We are delighted to announce our plenary speakers for #MicroSeq2025! Dr Rose Collis, Dr Jackie Mahar, Dr Peter Mee, and Dr Leah Roberts! We’ll be treated to four excellent talks across September 3-4. We can’t wait! Register below👇
trybooking.com/events/landing/1424679
trybooking.com/events/landing/1424679
August 7, 2025 at 2:37 AM
We are delighted to announce our plenary speakers for #MicroSeq2025! Dr Rose Collis, Dr Jackie Mahar, Dr Peter Mee, and Dr Leah Roberts! We’ll be treated to four excellent talks across September 3-4. We can’t wait! Register below👇
trybooking.com/events/landing/1424679
trybooking.com/events/landing/1424679
Reposted by Wytamma
🏆 #MicroSeq2025 has plenty of awards on offer! 💰 Cash prizes for best talks are sponsored by @aussocmic.bsky.social, @ausvirologysoc.bsky.social, and #MGen.
Plus, loads of merch on offer for the best question of each session! 🖊️📔
Register to submit an abstract👇
trybooking.com/events/landing/1424679
Plus, loads of merch on offer for the best question of each session! 🖊️📔
Register to submit an abstract👇
trybooking.com/events/landing/1424679
August 5, 2025 at 2:48 AM
🏆 #MicroSeq2025 has plenty of awards on offer! 💰 Cash prizes for best talks are sponsored by @aussocmic.bsky.social, @ausvirologysoc.bsky.social, and #MGen.
Plus, loads of merch on offer for the best question of each session! 🖊️📔
Register to submit an abstract👇
trybooking.com/events/landing/1424679
Plus, loads of merch on offer for the best question of each session! 🖊️📔
Register to submit an abstract👇
trybooking.com/events/landing/1424679
Reposted by Wytamma
VIPERA v1.2.2 is out!! 🐍
now you can swap in different stats (useful for non-linear allele freq trends). also: new Docker images on release, containerized CI, updated envs, and minor bug fixes for smoother, reproducible intra-patient SARS-CoV-2 analyses
🧪👉 github.com/PathoGenOmics-Lab/VIPERA
now you can swap in different stats (useful for non-linear allele freq trends). also: new Docker images on release, containerized CI, updated envs, and minor bug fixes for smoother, reproducible intra-patient SARS-CoV-2 analyses
🧪👉 github.com/PathoGenOmics-Lab/VIPERA
GitHub - PathoGenOmics-Lab/VIPERA: A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis
A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis - PathoGenOmics-Lab/VIPERA
github.com
July 30, 2025 at 7:53 AM
VIPERA v1.2.2 is out!! 🐍
now you can swap in different stats (useful for non-linear allele freq trends). also: new Docker images on release, containerized CI, updated envs, and minor bug fixes for smoother, reproducible intra-patient SARS-CoV-2 analyses
🧪👉 github.com/PathoGenOmics-Lab/VIPERA
now you can swap in different stats (useful for non-linear allele freq trends). also: new Docker images on release, containerized CI, updated envs, and minor bug fixes for smoother, reproducible intra-patient SARS-CoV-2 analyses
🧪👉 github.com/PathoGenOmics-Lab/VIPERA
Our study on SARS-CoV-2 dynamics and long COVID in Nepal has made it to preprint 🎉 Huge thanks everyone from BNMT, Center for Molecular Dynamics Nepal (CMDN), and the Centre for Pathogen Genomics at The Peter Doherty Institute for Infection and Immunity 👏👏👏
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
The geospatial phylodynamics of SARS-CoV-2 in Nepal and clinical phenotype of long COVID during the Delta-Omicron waves
The COVID-19 pandemic exposed gaps in global emerging infectious disease preparedness, particularly for countries with high levels of economic migration, such as Nepal. The Epidemic Intelligence proje...
www.medrxiv.org
July 26, 2025 at 5:17 AM
Our study on SARS-CoV-2 dynamics and long COVID in Nepal has made it to preprint 🎉 Huge thanks everyone from BNMT, Center for Molecular Dynamics Nepal (CMDN), and the Centre for Pathogen Genomics at The Peter Doherty Institute for Infection and Immunity 👏👏👏
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Had a great time at #SMBE2025 presenting our work of bacterial genome classification with AI github.com/bloodhound-d...
July 24, 2025 at 6:57 AM
Had a great time at #SMBE2025 presenting our work of bacterial genome classification with AI github.com/bloodhound-d...
Reposted by Wytamma
🦋Hello BlueSky!🦋 Let's get right into it. MicroSeq is back September 3-4, 2025! Stay tuned for more details on registration and abstract submission coming soon here and at www.microseqconference.com. 🌟Save the date!🌟
#MicroSeq2025
#MicroSeq2025
July 3, 2025 at 5:47 AM
🦋Hello BlueSky!🦋 Let's get right into it. MicroSeq is back September 3-4, 2025! Stay tuned for more details on registration and abstract submission coming soon here and at www.microseqconference.com. 🌟Save the date!🌟
#MicroSeq2025
#MicroSeq2025
Reposted by Wytamma
BEAST X v10.5.0 finally released – you can't just do beta releases forever. github.com/beast-dev/be...
Details and instructions for installing on the BEAST website: beast.community
Details and instructions for installing on the BEAST website: beast.community
July 2, 2025 at 8:32 PM
BEAST X v10.5.0 finally released – you can't just do beta releases forever. github.com/beast-dev/be...
Details and instructions for installing on the BEAST website: beast.community
Details and instructions for installing on the BEAST website: beast.community
Reposted by Wytamma
Only the fourth case of ABLV in humans. Although ABLV is classified as a different species to rabies virus, the disease is more of less rabies: www.health.nsw.gov.au/news/Pages/2...
News - Community urged not to touch bats after rare case of Australian bat lyssavirus
NSW Health confirms first bat lyssavirus case in 2025. Avoid handling bats and seek urgent care if bitten or scratched. Only trained experts should manage injured bats.
www.health.nsw.gov.au
July 2, 2025 at 6:35 AM
Only the fourth case of ABLV in humans. Although ABLV is classified as a different species to rabies virus, the disease is more of less rabies: www.health.nsw.gov.au/news/Pages/2...
Reposted by Wytamma
Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen...
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
June 10, 2025 at 4:27 PM
Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen...
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
Reposted by Wytamma
📢Today Pathoplexus announces the inclusion of 2 new viral pathogens: RSV (A & B) and HMPV.
These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.
1/4
These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.
1/4
May 22, 2025 at 4:06 PM
📢Today Pathoplexus announces the inclusion of 2 new viral pathogens: RSV (A & B) and HMPV.
These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.
1/4
These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.
1/4
Please move genomes to an open pathogen platform like pathoplexus.org!
May 29, 2025 at 5:08 AM
Please move genomes to an open pathogen platform like pathoplexus.org!
Reposted by Wytamma
Hello binfies 👋!
There is an open position for a senior bioinformatician to join our fab **core bioinformatics** team at @quadraminstitute.bsky.social.
jobs.quadram.ac.uk/Details.asp?...
There is an open position for a senior bioinformatician to join our fab **core bioinformatics** team at @quadraminstitute.bsky.social.
jobs.quadram.ac.uk/Details.asp?...
April 10, 2025 at 8:31 AM
Hello binfies 👋!
There is an open position for a senior bioinformatician to join our fab **core bioinformatics** team at @quadraminstitute.bsky.social.
jobs.quadram.ac.uk/Details.asp?...
There is an open position for a senior bioinformatician to join our fab **core bioinformatics** team at @quadraminstitute.bsky.social.
jobs.quadram.ac.uk/Details.asp?...
Prompt injection is a feature not a bug
April 1, 2025 at 6:17 AM
Prompt injection is a feature not a bug
Reposted by Wytamma
🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again!
forms.gle/YJP6WQjsk8KK...
forms.gle/YJP6WQjsk8KK...
Snippy: Microbial Variant Calling Community Survey
Help us drive the next wave of innovation in Single-Nucleotide Polymorphism (SNP) discovery and genome analysis by sharing your valuable experiences and insights. This in-depth survey aims at understa...
forms.gle
March 4, 2025 at 9:04 AM
🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again!
forms.gle/YJP6WQjsk8KK...
forms.gle/YJP6WQjsk8KK...
How much did this bad boy cost to make? Like low 10s of millions?
February 18, 2025 at 7:44 AM
How much did this bad boy cost to make? Like low 10s of millions?
Reposted by Wytamma
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...
rrwick.github.io/2025/02/07/d...
Medaka vs Dorado polish
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
February 7, 2025 at 4:20 AM
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...
rrwick.github.io/2025/02/07/d...
Introducing SciScroller 🔬 - it’s like TikTok for open scientific papers -> sciscroller.wytamma.com
SciScroller - Scroll Open Science
Explore and manage research papers in an innovative scrollable format. SciScroller makes academic discovery faster and easier.
sciscroller.wytamma.com
January 31, 2025 at 9:44 PM
Introducing SciScroller 🔬 - it’s like TikTok for open scientific papers -> sciscroller.wytamma.com
In the closing hours of the Anna’s Archive $10,000 dollar challenge there are a bunch of submissions rolling in. My favourite is Hypha A‘s Gilbert curve 🔥 -> archive.anarchy.cool/maps/isbn.html
Visualizing All ISBNs — $10k by 2025-01-31
This picture represents the largest fully open “list of books” ever assembled in the history of humanity.
annas-archive.org
January 30, 2025 at 9:53 PM
In the closing hours of the Anna’s Archive $10,000 dollar challenge there are a bunch of submissions rolling in. My favourite is Hypha A‘s Gilbert curve 🔥 -> archive.anarchy.cool/maps/isbn.html