Chris Kent
@chris.primalscheme.com
PhD student in the Quick Lab with @articnetwork.bsky.social
Reposted by Chris Kent
🎉 New in August: Measles virus joins Pathoplexus!
Following strong community support, we added MeV data submission (with Open & Restricted-Use options, as always) and powerful search & data access for MeV
pathoplexus.org/measles/search
5/10
Following strong community support, we added MeV data submission (with Open & Restricted-Use options, as always) and powerful search & data access for MeV
pathoplexus.org/measles/search
5/10
August 27, 2025 at 3:57 PM
🎉 New in August: Measles virus joins Pathoplexus!
Following strong community support, we added MeV data submission (with Open & Restricted-Use options, as always) and powerful search & data access for MeV
pathoplexus.org/measles/search
5/10
Following strong community support, we added MeV data submission (with Open & Restricted-Use options, as always) and powerful search & data access for MeV
pathoplexus.org/measles/search
5/10
Reposted by Chris Kent
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 Chris Kent
A few days ago we preprinted our Freyja 2 paper, describing the expansion of our original Freyja method to a real-time, multi-pathogen surveillance tool to track pathogen lineage prevalence and dynamics from sequencing of wastewater and other complex samples (like milk). 🧵
doi.org/10.1101/2025...
doi.org/10.1101/2025...
Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2
Case-based infectious disease surveillance is fundamental to public health, but is resource-intensive, logistically complex, and prone to sampling bias. Wastewater testing and sequencing have increasi...
doi.org
July 31, 2025 at 7:18 PM
A few days ago we preprinted our Freyja 2 paper, describing the expansion of our original Freyja method to a real-time, multi-pathogen surveillance tool to track pathogen lineage prevalence and dynamics from sequencing of wastewater and other complex samples (like milk). 🧵
doi.org/10.1101/2025...
doi.org/10.1101/2025...
need an (artic)help-ing hand with enzyme availability for amplicon sequencing? 🧬 check out this new preprint from @annakovalenko.bsky.social featuring a new norovirus-gii scheme!
doi.org/10.1101/2025...
doi.org/10.1101/2025...
June 15, 2025 at 8:16 PM
need an (artic)help-ing hand with enzyme availability for amplicon sequencing? 🧬 check out this new preprint from @annakovalenko.bsky.social featuring a new norovirus-gii scheme!
doi.org/10.1101/2025...
doi.org/10.1101/2025...
Reposted by Chris Kent
New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon
github.com/bede/deacon
Deacon: fast sequence filtering and contaminant depletion https://www.biorxiv.org/content/10.1101/2025.06.09.658732v1
June 13, 2025 at 1:25 PM
New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon
github.com/bede/deacon
Reposted by Chris Kent
Absolutely thrilled to announce the launch of ARTIC2 - a £5.5M 5 year project funded by @wellcometrust.bsky.social to build on the ARTIC approach of low-cost, globally accessible genome sequencing for surveillance of outbreaks, epidemics and endemic diseases: www.birmingham.ac.uk/news/2025/am...
Ambitious project to develop low-cost genome sequencing for pathogens known and unknown - University of Birmingham
Project will build on research that helped diagnostic labs to adopt sequencing capacity for COVID-19 and permit characterisation of future infectious threats
www.birmingham.ac.uk
May 22, 2025 at 10:57 AM
Absolutely thrilled to announce the launch of ARTIC2 - a £5.5M 5 year project funded by @wellcometrust.bsky.social to build on the ARTIC approach of low-cost, globally accessible genome sequencing for surveillance of outbreaks, epidemics and endemic diseases: www.birmingham.ac.uk/news/2025/am...
Reposted by Chris Kent
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 Chris Kent
First genome sequence from the Ugandan Ebolavirus outbreak with analysis: virological.org/t/990 and first filovirus genome submitted to Pathoplexus database: pathoplexus.org/seq/PP_0011C.... Great (and rapid) work from the National Health Laboratory, UVRI and partners.
Near Real-Time Genomic Characterization of the 2025 Sudan Ebolavirus Outbreak in Uganda’s Index Case: Insights into Evolutionary Origins
Introduction Case History: On January 30, 2025, the Ministry of Health declared an outbreak of Sudan Ebola Virus (SUDV) Disease in Kampala, Uganda, following the death of a healthcare worker at Mula...
virological.org
February 3, 2025 at 4:32 PM
First genome sequence from the Ugandan Ebolavirus outbreak with analysis: virological.org/t/990 and first filovirus genome submitted to Pathoplexus database: pathoplexus.org/seq/PP_0011C.... Great (and rapid) work from the National Health Laboratory, UVRI and partners.
Reposted by Chris Kent
I'm putting together a Microbial Bioinformatics starter pack to help get everyone connected in our community. Let me know if there are any bluesky users to be added and share so that twitter refugees can tune back in to the fantastic world microbes go.bsky.app/3ezLo7e
January 10, 2025 at 9:38 AM
I'm putting together a Microbial Bioinformatics starter pack to help get everyone connected in our community. Let me know if there are any bluesky users to be added and share so that twitter refugees can tune back in to the fantastic world microbes go.bsky.app/3ezLo7e
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...
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 Chris Kent
ARTIC have primers for #Marburg virus! (MVD)
labs.primalscheme.com/detail/artic...
#molecularepidemiology #pathogen #pathogensurviellance #bioinformatics #epidemiology #virus #outbreak #clinicalvirology
labs.primalscheme.com/detail/artic...
#molecularepidemiology #pathogen #pathogensurviellance #bioinformatics #epidemiology #virus #outbreak #clinicalvirology
labs.primalscheme.com
November 13, 2024 at 4:12 PM
ARTIC have primers for #Marburg virus! (MVD)
labs.primalscheme.com/detail/artic...
#molecularepidemiology #pathogen #pathogensurviellance #bioinformatics #epidemiology #virus #outbreak #clinicalvirology
labs.primalscheme.com/detail/artic...
#molecularepidemiology #pathogen #pathogensurviellance #bioinformatics #epidemiology #virus #outbreak #clinicalvirology
Very excited to be using the soon-to-be released MK1D for HBV sequencing from Uganda!
May 25, 2024 at 9:18 AM
Very excited to be using the soon-to-be released MK1D for HBV sequencing from Uganda!