Finlay Maguire

Releases · tseemann/abricate :mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes - tseemann/abricate

💾 ABRicate 1.2.0 has been released!

This 'oversight' lasted 6 years, but with help from @finlaym.bsky.social we got CI working and updated all the databases. #bioconda #conda #bioinformatics #microbiology #genomics

github.com/tseemann/abr...

On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5

The associated slogan of "where infinite ambition meets global impact" being mostly evocative of futility ("where an unstoppable force meets an immovable object") also contributes to this feeling.

New vs old Dalhousie logo

Probably should have seen this coming when they expensively redesigned the logo to detach the head from the rest of the body.

The associated slogan of "where infinite ambition meets global impact" being mostly evocative of futility ("where an unstoppable force meets an immovable object") also contributes to this feeling.

New vs old Dalhousie logo

Probably should have seen this coming when they expensively redesigned the logo to detach the head from the rest of the body.

"My mantra is transparency, fairness and equity" nothing more transparent, fair, and equitable than unilaterally locking out faculty and refusing to negotiate.

The Dal "Labour Relations" page indicating that the "latest news" and "latest updates" were all August 20 when they locked out DFA members.

Six days.

Six days with no news for students or locked out faculty, counsellors, and librarians.

Six days with no news for other staff, community partners, or research collaborators at other univs.

Six days of the senior admin doing nothing.

15 days since the admin was at the bargaining table.

"The lockout comes after 83 per cent of DFA members voted to reject the school’s latest contract offer." - I think you'll find it actually came before CTV...

Bit disappointed at the publicly non-partisan stance from the DSU president.

I gave a symposium talk at the European Society for Evolutionary Biology 2025 (#eseb2025) meeting last week and this was my title slide showcasing how I was speaking as an independent scientist because @dalhousieu.bsky.social @dalhousie.bsky.social has locked us out.

Here’s where we stand:

My union moved on salary and was willing to talk: Dal mgmnt was not interested

My union offered to find ways to save money: Mgmnt said no.

My union wanted to work together to build new child care: Mgmnt didn’t care.

Let’s #KeepDalStrong, we said. No, they replied.

Early innate immune response and evolution of a SARS-CoV-2 furin cleavage site inactive variant in bat cells Baid et al. show that insectivorous E. fuscus bat cells have evolved an advantageous early innate immune response to SARS-CoV-2 infection relative to human cells. Additionally, they extend molecular e...

🚨Second study from the lab. @CellReports
SARS-CoV- and SARS-CoV-2-like viruses are found in insectivorous bats, but the antiviral responses in these bats remain less studied. Here we show how bat cells respond to SARS-CoV-2 and shed light on virus entry.
www.cell.com/cell-reports... #LZCI

It may not be worth much right now but this campaign still holds true.

WildEpi was well represented at the One Health - AMR and Zoonosis meeting in Calgary. Dr. Samira Mubareka and Dr. Finlay Maguire.
@smubareka.bsky.social @finlaym.bsky.social

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...

🦘✂️ 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...

Pathoplexus| Home Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

📢 We're excited to introduce Pathoplexus, a specialized sequence database for human viral pathogens! 🌍 🧬
Launching with 4 viruses, Pathoplexus.org combines modern open-source software with transparent governance to improve global pathogen sequence sharing.

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Francis Chikuse on Africa PGI mammoth priority pathogens prioritisation process. Process driven through 4 expert groups: Malaria, AMR (chaired by Iruka Okeke), foodborne diseases, vaccine preventable diseases. Priority AMR projects: Neonatal sepsis, invasive salmonella typhi, one health.

Final talk in our harmonizing pathogen data collection from Zetty Jamaluddin (UKM) on hAMRonized (github.com/pha4ge/hAMRo...) AMRfinderplus analysis via Google Colab
zenodo.org/record/6438173 with recent extensions for batch and microreact Viz. Used in Malaysia with global workshop participants!

Patiyan Anderson (MDU-PHL) on AusPathoGen umbrella with data management and Viz via AusTrakka (www.cdgn.org.au/austrakka). Need to optimise data collection to inform surveillance. Core+pathogen specific data driven by end-goal analyses (aiding buy-in and actually having actionable data).

Jillian Paull (Broad) on PHA4GE's wastewater contextual data specification. Making sure investment in WW capacity is not wasted by bad data. Machine readability, interoperability to other specs, reuse of terms from pubmed.ncbi.nlm.nih.gov/35169842/, & input from HIC/LMIC folks across disciplines.

Bryan Wee (Roslin) on contextual data for Uganda One Health AMR digital-one-health.github.io w/ red, yellow, green tags for sensitivity and harmonisation of data from ag, env, & clinic. Multidisciplinary data meeting to inform metadata specification (w/ PHA4GE recs) before pilot E. coli seq project.

Gerald Mboowa (AfricaCDC): 10 genomics centers for excellence coming w/ ACEGID/SANBI/KRISP bioinf support. 2019-2023: only 7 countries with WGS to only 7 without. ONT&Ill diversify the risk of reagent access issues. Federated African Pathogen Data Sharing & Archive to try and solve data challenges.

Abebe Negeri (Ethiopian Public Health Institute) new Pathogen Genomics Core Facility est. 2021, largely SC2 so far but plans for HIV, TB, polio, AMR, IPAC etc. Integration of multiple programs key for sustainability and making most of a core. Need for full time staff and well-defined career paths!

Kim Ng (SSI) on IT challenges scaling infrastructure and new MicrobeSeq initiative
microbeseqen.ssi.dk/about-microb... federating regional and SSI HPC based on IRIDA, microreact, galaxy, nextflow, ansible, git, and PHA4GE/elixir standards/recommendations. Key message: don't reinvent the wheel!

Ten recommendations for supporting open pathogen genomic analysis in public health - Nature Medicine To support progress in genomic epidemiology, a transparent, user-friendly approach is required.

Day 2 of #pha4gecon: Sarah Hersey (Head of WHO IPSN) chairing resource limited infra for pathobioinf. First Joel Sevinsky, building on www.nature.com/articles/s41... Terra+theaigen wfs FISMA/FedRAMP compliant example. Cloud costs 1-2% of consumables. New Theaigen Global Health Initiative non-profit

GitHub - oschwengers/bakta: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Rapid & standardized annotation of bacterial genomes, MAGs & plasmids - GitHub - oschwengers/bakta: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Vincent Rennie and Annelies van Rie on MAGMA Automated mapping of transmission hotspots, treatment recommendations, and phylogenetic cluster selection: www.medrxiv.org/content/10.1..., @oschwengers.bsky.social on Bakta's recent updates and gene name harmonisation efforts (github.com/oschwengers/...)

Lightning talks: Hiba Aribi on new RNA analysis tool github.com/omicscodeath.... Nouhaila En najih: SC2 phylotools comparison. Thibaut Cherif: Guinea's One Health AMR. Emma Griffiths: PHA4GE's data standard registry (includes incorporating non-PHA4GE data standards). Lam-Kwong: Hong Kong SC2 db

Alan Christoffels kicks off the first PHA4GE conference in beautiful Stellenbosch, with a wonderful opening keynote from Anita Ghansah #PHA4GEcon

Katrina Kalantar (CZID) on their cloud metagenomics workflows characterising the taxonomy, AMR (w/ RGI), & consensus sequences (github.com/chanzuckerbe...). Takeaways: Inference of abundance and significance (v water control), RNA more sensitive than DNA, Sneathia as possible undernoticed pathogen.

Ilene Mizrachi (SRA head at NCBI) on the many excellent resources on NCBI e.g., datasets www.ncbi.nlm.nih.gov/datasets/, contamination screening suite, and >1.6m pathogen analyzed in NCBI pathogens with >1000 FDA regulatory actions, and NCBI virus (e.g., www.biorxiv.org/content/10.1... and VADR).