Josh Quick
@scalene.bsky.social
UKRI Future Leaders Fellow, University of Birmingham
Reposted by Josh Quick
Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it:
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
October 23, 2025 at 8:16 PM
Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it:
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
Reposted by Josh Quick
Interested in respiratory metagenomics? We assembled nearly all of the virus genomes in a respiratory verification panel manufactured by ZeptoMetrix.
Blog: artic.network/2025-07-26_p...
Assemblies: github.com/bede/zmrp
@scalene.bsky.social @pathogenomenick.bsky.social @articnetwork.bsky.social
Blog: artic.network/2025-07-26_p...
Assemblies: github.com/bede/zmrp
@scalene.bsky.social @pathogenomenick.bsky.social @articnetwork.bsky.social
Genome assemblies for a respiratory metagenomics positive control | ARTIC network - pathogen genomics from sample to response
artic.network
August 12, 2025 at 8:14 AM
Interested in respiratory metagenomics? We assembled nearly all of the virus genomes in a respiratory verification panel manufactured by ZeptoMetrix.
Blog: artic.network/2025-07-26_p...
Assemblies: github.com/bede/zmrp
@scalene.bsky.social @pathogenomenick.bsky.social @articnetwork.bsky.social
Blog: artic.network/2025-07-26_p...
Assemblies: github.com/bede/zmrp
@scalene.bsky.social @pathogenomenick.bsky.social @articnetwork.bsky.social
Reposted by Josh Quick
We’re continuing to expand the number of pathogens we support for Freyja (github.com/andersen-lab...), and developing corresponding low-cost and highly sensitive amplicon sequencing schemes as our Modjadji initiative (including @scalene.bsky.social and @chris.primalscheme.com
GitHub - andersen-lab/Freyja-barcodes
Contribute to andersen-lab/Freyja-barcodes development by creating an account on GitHub.
github.com
July 31, 2025 at 7:18 PM
We’re continuing to expand the number of pathogens we support for Freyja (github.com/andersen-lab...), and developing corresponding low-cost and highly sensitive amplicon sequencing schemes as our Modjadji initiative (including @scalene.bsky.social and @chris.primalscheme.com
Francisella tularensis identified using @articnetwork.bsky.social SMART-9N metagenomics and @nanoporetech.com sequencing. Amazing work!
🚨 Tularemia mystery solved in stranded belugas in Alaska! thanks to smart-9N metagenomics & nanopore sequencing 🔬🐋 #wildhealth #onehealth Well done @bortz-virology.bsky.social and Team!!
wwwnc.cdc.gov/eid/article/...
wwwnc.cdc.gov/eid/article/...
June 19, 2025 at 10:27 AM
Francisella tularensis identified using @articnetwork.bsky.social SMART-9N metagenomics and @nanoporetech.com sequencing. Amazing work!
Click the link for open-source recipes for end-preparation, barcode and adapter ligation. 60% cost saving over commercial kits for the ARTIC protocol.
the link to the preprint 🔗 www.biorxiv.org/content/10.1...
Reducing Supply Chain Dependencies for Viral Genomic Surveillance: Get by with a Little HELP from Commercial Enzymes already in your Lab Freezer
The COVID-19 pandemic exposed vulnerabilities in global laboratory supply chains, disrupting genomic surveillance efforts essential to epidemic response. To address this challenge, we developed ARTIC ...
www.biorxiv.org
June 19, 2025 at 10:02 AM
Click the link for open-source recipes for end-preparation, barcode and adapter ligation. 60% cost saving over commercial kits for the ARTIC protocol.
Reposted by Josh Quick
Ever had to pause genomic surveillance due to enzyme shortages?🫣 Happy to share our new preprint with the solution inside 🦹♀️💪 biorxiv.org/content/10.110…
@scalene.bsky.social @chris.primalscheme.com @pathogenomenick.bsky.social @articnetwork.bsky.social @nanoporetech.com
@scalene.bsky.social @chris.primalscheme.com @pathogenomenick.bsky.social @articnetwork.bsky.social @nanoporetech.com
https://biorxiv.org/content/10.110…
June 15, 2025 at 6:21 PM
Ever had to pause genomic surveillance due to enzyme shortages?🫣 Happy to share our new preprint with the solution inside 🦹♀️💪 biorxiv.org/content/10.110…
@scalene.bsky.social @chris.primalscheme.com @pathogenomenick.bsky.social @articnetwork.bsky.social @nanoporetech.com
@scalene.bsky.social @chris.primalscheme.com @pathogenomenick.bsky.social @articnetwork.bsky.social @nanoporetech.com
Reposted by Josh Quick
And don't forget to watch the accompanying video of @scalene.bsky.social broodily walking the canals of Birmingham describing how sequencing can be useful in outbreaks: www.youtube.com/watch?embeds...
Changing how the world tracks emerging viruses | University of Birmingham
YouTube video by University of Birmingham
www.youtube.com
May 22, 2025 at 12:05 PM
And don't forget to watch the accompanying video of @scalene.bsky.social broodily walking the canals of Birmingham describing how sequencing can be useful in outbreaks: www.youtube.com/watch?embeds...
Job opportunity working with myself and @pmoyniha.bsky.social on an exciting Gates funded project developing TB lysis enzymes for rapid diagnostics. edzz.fa.em3.oraclecloud.com/hcmUI/Candid...
Research Associate (Genomics) - School of Biosciences - 105316 - Grade 6
The successful candidate will play a crucial role in developing an innovative TB diagnostic approach, collaborating across a multidisciplinary team to advance our novel enzymatic lysis technology. Key...
edzz.fa.em3.oraclecloud.com
April 8, 2025 at 10:42 AM
Job opportunity working with myself and @pmoyniha.bsky.social on an exciting Gates funded project developing TB lysis enzymes for rapid diagnostics. edzz.fa.em3.oraclecloud.com/hcmUI/Candid...
Reposted by Josh Quick
President Zelenskyy has been one of the greatest leaders of our time, guiding Ukraine through the darkest period of its recent history, rising up to Russia’s unwarranted aggression, being an inspiration to the Ukrainian people and ensuring that Ukraine’s voice is heard on the world stage.
February 20, 2025 at 12:14 AM
President Zelenskyy has been one of the greatest leaders of our time, guiding Ukraine through the darkest period of its recent history, rising up to Russia’s unwarranted aggression, being an inspiration to the Ukrainian people and ensuring that Ukraine’s voice is heard on the world stage.
Reposted by Josh Quick
Once again I am leaving the Munich Security Conference in a low mood. Amongst all the noise, the US signalled their plans for Europe, so things are becoming clearer. But things are clearly not good.
This is what we now know, and what we have to do about it:🧵1/17
This is what we now know, and what we have to do about it:🧵1/17
February 15, 2025 at 8:11 PM
Once again I am leaving the Munich Security Conference in a low mood. Amongst all the noise, the US signalled their plans for Europe, so things are becoming clearer. But things are clearly not good.
This is what we now know, and what we have to do about it:🧵1/17
This is what we now know, and what we have to do about it:🧵1/17
Reposted by Josh Quick
Working a treat here to, threw in some melt in nut inserts etc 😊
February 13, 2025 at 9:19 PM
Working a treat here to, threw in some melt in nut inserts etc 😊
Reposted by Josh Quick
Oh and Josh, I just wanted to let you know that I refer to your excellent 'lab-in-a-suitcase' work as a primary example of situations where the DIYNAFLUOR may find utility. It typically shows up in the first 1 or 2 slides of any presentation I make. 😅
February 12, 2025 at 9:58 PM
Oh and Josh, I just wanted to let you know that I refer to your excellent 'lab-in-a-suitcase' work as a primary example of situations where the DIYNAFLUOR may find utility. It typically shows up in the first 1 or 2 slides of any presentation I make. 😅
Built our first two DIYNAFLOURS and they work great! Thanks @willaanderson.bsky.social
February 12, 2025 at 4:11 PM
Built our first two DIYNAFLOURS and they work great! Thanks @willaanderson.bsky.social
Reposted by Josh Quick
Genotype D1.1 of H5N1 confirmed in Nevada cattle, which is the one circulating in birds and not B3.13, causing the wider cattle epizootic in the U.S.
In other words, this is a second observed jump from birds into cows.
Keep rolling the dice, shall we?
www.feedstuffs.com/agribusiness...
In other words, this is a second observed jump from birds into cows.
Keep rolling the dice, shall we?
www.feedstuffs.com/agribusiness...
New HPAI genotype found in Nevada dairy cows
APHIS confirms first detection of D1.1 genotype in dairy cattle through NMTS testing.
www.feedstuffs.com
February 5, 2025 at 7:31 PM
Genotype D1.1 of H5N1 confirmed in Nevada cattle, which is the one circulating in birds and not B3.13, causing the wider cattle epizootic in the U.S.
In other words, this is a second observed jump from birds into cows.
Keep rolling the dice, shall we?
www.feedstuffs.com/agribusiness...
In other words, this is a second observed jump from birds into cows.
Keep rolling the dice, shall we?
www.feedstuffs.com/agribusiness...
Reposted by Josh Quick
The @universityofleeds.bsky.social is the first Russell Group Uni to quit X! 🎉 🎉
Read more👇
tinyurl.com/2h3tyjfx
@lsjleeds.bsky.social
#Yorkshire #Leeds #Academia #AcademicSky #HigherEd #LawSky
Read more👇
tinyurl.com/2h3tyjfx
@lsjleeds.bsky.social
#Yorkshire #Leeds #Academia #AcademicSky #HigherEd #LawSky
Leeds becomes first Russell Group university to quit X - Research Professional News
Leeds says Elon Musk’s social media site “no longer aligns with our university values”
tinyurl.com
January 23, 2025 at 4:11 PM
The @universityofleeds.bsky.social is the first Russell Group Uni to quit X! 🎉 🎉
Read more👇
tinyurl.com/2h3tyjfx
@lsjleeds.bsky.social
#Yorkshire #Leeds #Academia #AcademicSky #HigherEd #LawSky
Read more👇
tinyurl.com/2h3tyjfx
@lsjleeds.bsky.social
#Yorkshire #Leeds #Academia #AcademicSky #HigherEd #LawSky
Reposted by Josh Quick
The world’s richest man is promoting the far right in Europe. Don’t buy a Tesla
.
Location: Tesla Gigafactory, Berlin
www.youtube.com/watch?v=NjWl...
.
Location: Tesla Gigafactory, Berlin
www.youtube.com/watch?v=NjWl...
Heil Tesla
YouTube video by Led By Donkeys
www.youtube.com
January 23, 2025 at 2:42 PM
The world’s richest man is promoting the far right in Europe. Don’t buy a Tesla
.
Location: Tesla Gigafactory, Berlin
www.youtube.com/watch?v=NjWl...
.
Location: Tesla Gigafactory, Berlin
www.youtube.com/watch?v=NjWl...
Reposted by Josh Quick
President Trump will learn pretty soon that Putin cannot be convinced with money, at least not any more. He is the richest person in Russia already, though he will never say no to more billions, but that wasn't the point of him starting the full scale war in Ukraine. (Thread)
January 22, 2025 at 7:18 PM
President Trump will learn pretty soon that Putin cannot be convinced with money, at least not any more. He is the richest person in Russia already, though he will never say no to more billions, but that wasn't the point of him starting the full scale war in Ukraine. (Thread)
Really glad this is out there; a lot has happened in the 7 years since the original paper including:
-67,000 schemes designed by the community
-18M genome sequences using PrimalScheme
-67,000 schemes designed by the community
-18M genome sequences using PrimalScheme
Fancy some light Christmas reading? I’m happy to share our new preprint, covering the impact and cutting edge improvements to PrimalScheme!
Preprint: www.biorxiv.org/content/10.1...
Preprint: www.biorxiv.org/content/10.1...
PrimalScheme: open-source community resources for low-cost viral genome sequencing
Viral genome sequencing using the ARTIC protocol has been a vital tool for understanding the spread of epidemics including Ebola, Zika, COVID-19 and Mpox and has seen widespread adoption due to its lo...
www.biorxiv.org
December 24, 2024 at 9:16 PM
Really glad this is out there; a lot has happened in the 7 years since the original paper including:
-67,000 schemes designed by the community
-18M genome sequences using PrimalScheme
-67,000 schemes designed by the community
-18M genome sequences using PrimalScheme
Reposted by Josh Quick
Fancy some light Christmas reading? I’m happy to share our new preprint, covering the impact and cutting edge improvements to PrimalScheme!
Preprint: www.biorxiv.org/content/10.1...
Preprint: www.biorxiv.org/content/10.1...
PrimalScheme: open-source community resources for low-cost viral genome sequencing
Viral genome sequencing using the ARTIC protocol has been a vital tool for understanding the spread of epidemics including Ebola, Zika, COVID-19 and Mpox and has seen widespread adoption due to its lo...
www.biorxiv.org
December 23, 2024 at 10:37 AM
Fancy some light Christmas reading? I’m happy to share our new preprint, covering the impact and cutting edge improvements to PrimalScheme!
Preprint: www.biorxiv.org/content/10.1...
Preprint: www.biorxiv.org/content/10.1...
Reposted by Josh Quick
primalscheme3 is now live at primalscheme.com!
Key features
- Handle up to 20% target diversity
- Create panels for multiple targets
- Improved multiplexing, allowing 10x more primer per reaction
Preprint to follow
Key features
- Handle up to 20% target diversity
- Create panels for multiple targets
- Improved multiplexing, allowing 10x more primer per reaction
Preprint to follow
PrimalScheme3: primer panels for multiplex PCR
primalscheme is a tool for designing primer panels for multiplex PCR. It uses a greedy algorithm to find primers for tiling amplicon generation for multiple reference genomes.
primalscheme.com
December 9, 2024 at 2:25 PM
primalscheme3 is now live at primalscheme.com!
Key features
- Handle up to 20% target diversity
- Create panels for multiple targets
- Improved multiplexing, allowing 10x more primer per reaction
Preprint to follow
Key features
- Handle up to 20% target diversity
- Create panels for multiple targets
- Improved multiplexing, allowing 10x more primer per reaction
Preprint to follow
Reposted by Josh Quick
Today Pathoplexus announces the inclusion of a new viral pathogen: mpox (previously known as monkeypox).
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
December 9, 2024 at 7:15 PM
Today Pathoplexus announces the inclusion of a new viral pathogen: mpox (previously known as monkeypox).
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
Thank you for doing this it's going to be incredibly useful!
Hey #HiSciSky 👋.
I'm a post-doc researcher with a background in scientific device dev.
I have just released an open-source STEM-Education project for a $40, 3D-printed, DNA fluorometer with ng/uL levels of sensitivity. Follow for updates!
GitHub Repo: github.com/traulab/DIYN...
#DIYNAFLUOR #STEM
I'm a post-doc researcher with a background in scientific device dev.
I have just released an open-source STEM-Education project for a $40, 3D-printed, DNA fluorometer with ng/uL levels of sensitivity. Follow for updates!
GitHub Repo: github.com/traulab/DIYN...
#DIYNAFLUOR #STEM
December 9, 2024 at 4:39 PM
Thank you for doing this it's going to be incredibly useful!
Reposted by Josh Quick
Disease prevalence in US states before & after vaccine introduction
Graphic from Edward Tufte
More graphics.wsj.com/infectious-d... 🧪
Graphic from Edward Tufte
More graphics.wsj.com/infectious-d... 🧪
November 15, 2024 at 5:00 AM
Disease prevalence in US states before & after vaccine introduction
Graphic from Edward Tufte
More graphics.wsj.com/infectious-d... 🧪
Graphic from Edward Tufte
More graphics.wsj.com/infectious-d... 🧪
Reposted by Josh Quick
For a few years I've been thinking about calling somatic mutations without matched normals using long read haplotypes. I've posted a preprint with my experiments to explore when this works (and when it doesn't) and developing a prototype mutation caller ("smrest"): www.biorxiv.org/content/10.1...
February 29, 2024 at 2:59 PM
For a few years I've been thinking about calling somatic mutations without matched normals using long read haplotypes. I've posted a preprint with my experiments to explore when this works (and when it doesn't) and developing a prototype mutation caller ("smrest"): www.biorxiv.org/content/10.1...