🎉 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

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

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...

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...

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

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...

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...

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.

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...

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

ARTIC have primers for #Marburg virus! (MVD)

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!