Jana Batovska

Screenshot of podcast website

Folks been asking for a searchable catalogue for microbinfie podcast. With a 147 episodes, and 78+ guests its getting hard to find episodes of your interest.

anyway, i wrote a catalogue

https://www.happykhan.com/microbinfie

see all our lovely guests at https://www.happykhan.com/microbinfie/guests

Automated annotation and validation of human respiratory virus sequences using VADR Abstract. Accurate annotation of viral genomes is essential for reliable downstream analysis and public data sharing. While National Center for Biotechnolo

From #OUP 's #DATABASE journal | Automated annotation and validation of human respiratory #virus sequences using VADR | #Bioinformatics #Genomics #OpenScience #OpenSource 🧬 🖥️ 🧪 🔓
⬇️
academic.oup.com/database/art...

Determining the value of genomics in healthcare - Nature Medicine Assessing the value of genomics is key to informing evidence-based policies; this Review outlines how current approaches to health technology assessment, implementation and data management can be adap...

In this Nature Medicine paper, we draw from our experiences in evaluating and implementing #genomics in Australia, Canada, England, Hong Kong and the US

www.nature.com/articles/s41...

Making genomic data FAIR through effective Data Portals - Scientific Data Genomic data portals collect, annotate, and make data files available to researchers and, increasingly, AI algorithms. They are run by, among others, broad data archive repositories or consortium-spec...

From the @ucscgenomics.bsky.social team in @natureportfolio.nature.com #scientificdata | Making genomic data FAIR through effective Data Portals | #FAIR #OpenScience #Bioinformatics #Genomics 🧬 🖥️ 🧪 🔓 CC/ @ebi.embl.org @mdperry.bsky.social
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www.nature.com/articles/s41...

Come see my poster at IMMEM Poster 151.

🔬 QualiBact – provides robust, data-driven QC thresholds for 304 bacterial species, built from >2.4M assemblies (AllTheBacteria + RefSeq).
⚙️ SpecCheck – an open-source command-line tool that applies these standards […]

[Original post on mstdn.science]

🎉 Excited to announce that the 25th Annual Scientific Meeting of the Australian Society for Antimicrobials – Antimicrobials 2026 – will be held from 26–28 February 2026 at the Adelaide Convention Centre

📅 Save the date and stay tuned for program highlights!

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...

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes Abstract. Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is st

🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...

📢Health alert: #JapaneseEncephalitis virus detected in mosquitos in rural Victoria (Horsham), the first detection in the 2025/26 season
Protect yourself:
✔️ Repellent
✔️ Cover up
✔️ Avoid dawn/dusk bites
Free vaccine for high-risk groups
More info: bit.ly/4omYE0l

Registration is now open! 🎉

Be part of the 2026 One Health Microbiome Center Symposium at Penn State (May 13–14). Explore microbiomes across health & ecosystems and connect with top researchers.

Sign up here:

www.eventbrite.com/e/2026-one-h...

Early abstracts and travel awards close tomorrow

Last chance! Early abstracts & travel awards for #ASMicrobe close TOMORROW (Dec 2, 2 p.m. ET). Early submissions receive early review—helpful for planning travel & approvals. Submit today! ➜ asm.social/2Ij

Final presentation by Calum J. Walsh @calumwalsh.bsky.social
Rational Engineering of Live Bacterial Therapeutics from a Human Microbiome Biobank

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned

gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research Abstract. The rapid growth of metagenomic sequencing has generated an unprecedented wealth of metagenome-assembled genomes (MAGs), transforming opportuniti

GcMeta - a new global resource of metagenome-assembled genomes and their encoded functions with an easy to use, interactive and searchable website academic.oup.com/nar/advance-...

Public MAG datasets not available at NCBI or ENA Some metagenome assembled genome (MAG) datasets are not available in the standard locations (NCBI / ENA / etc) for a variety of reasons. Here you can contribute new ones you come across. To be recorde...

In the meantime, we've been collecting a list of these at tinyurl.com/mag-collecti.... Feel free to add more you find.

See also GlobDB from @daanspeth.bsky.social which incorporates some of these into a new MAG collection arxiv.org/abs/2506.11896

High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons - Microbiome Background High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. Results...

Still using 16S/ITS profiling? You might want to reconsider👀

Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable!
microbiomejournal.biomedcentral.com/articles/10....

Metalog: curated and harmonised contextual data for global metagenomics samples Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data

Great to see this finally published!

Metalog: curated and harmonised contextual data for global metagenomics samples

now out in @narjournal.bsky.social

academic.oup.com/nar/advance-...

A roadmap for equitable reuse of public microbiome data - Nature Microbiology In this Consensus Statement, a consortium of microbiome scientists discuss current sequencing data sharing policies and propose the use of a Data Reuse Information (DRI) tag to promote equitable and collaborative data sharing.

Our article on equitable reuse of public sequencing data is out! Led by @alexjprobst.bsky.social, @lhug.bsky.social, Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and myself -, co-authored by Anke Heyder, and developed in consultation with 167 scientists. tinyurl.com/n6yeanmk

Efficient and accurate search in petabase-scale sequence repositories - Nature MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

The Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...

MVIF Season 5 program

💫 #MVIF Season 5 💫

Feel free to join the keynotes by presenting your work–abstract submission is open:
www.microbiome-vif.org/en-US/how-to...

#MVIF is proudly supported by #illumina @corundumsb.bsky.social
and our non-commercial co-organizing partners Seerave Foundation @cunysph.bsky.social

Now @nidunn.bsky.social on importance of metadata for publishing and mobilising #metabarcoding data. Metadata key to understanding how species records were generated and making confidence judgement. FAIR #eDNA project has established workflow which @naturalengland.bsky.social have adopted #UKDNAWG25

Happy Thanksgiving everyone.
I will keep it short and sweet. Great news out of Brazil today 👇.
Congratulations to the interdisciplinary teams that made it a reality!

@mauriciolnogueira.bsky.social @astmh.bsky.social #Burantan

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

A flurry of snowflakes with text reading 'Virus Snowflakes: a collection of paper art viruses by Ed Hutchinson - Download now!' along with the logo of the MRC-University of Glasgow Centre for Virus Research

If you'd like to celebrate the biology of viruses - or the fight against viral diseases - this winter, try out our free and updated #VirusSnowflake designs.
Please share, and if you have any photos of Virus Snowflakes in your area it would be lovely to see them!
cvr-engagement.co.uk/virus-snowfl...

Are influenza B viruses really “human only”? New review synthesises evidence from serology & metagenomics for #IBV / IBV-like viruses in animals and aquatic hosts. One Health gaps remain. With @marioskoutsakos.viralvaxlab.com @duckswabber.bsky.social www.mdpi.com/1999-4915/17...

Variant Calling in the Goldilocks Zone: How Reference Genome Choice and Read Mapping Stringency Impact Heterozygosity Estimates and Phylogenetic Analyses The increasing numbers of published reference genomes and affordability of whole genome resequencing have enabled multispecies population genomic and phylogenomic studies on non-model organisms, but ....

Analysis of read mapping accuracy and efficiency, missing data, heterozygosity, and inferred phylogenies to evaluate the impact of reference #genome and read-mapping method onlinelibrary.wiley.com/doi/10.1111/...

Monumental effort led by Peter Simmonds and Jens Kuhn to reorganize the Family Flaviviridae based on analysis of RNA-directed RNA polymerase (RdRP) hallmark gene sequences is finally out. Enjoy reading. #ICTV @utmbhealth.bsky.social @astmh.bsky.social @sbvirologia.bsky.social

Join us for the #PHA4GECon2025 & #IPSNGPF2025 hosted by IPSN, @afro.who.int and @pha4ge.bsky.social.

Join our expert panel on October 27, 2025, as they tackle key genomics data challenges shaping global surveillance. Collaborate, share insights, and drive public health innovation.

ABSTRACT SUBMISSION and REGISTRATION IS NOW OPEN FOR THE 16TH AUSTRALIAN INFLUENZA SYMPOSIUM (13-14 November 2025 The Peter Doherty Institute for Infection and Immunity)
Registration link: eventbrite.com/e/16th-austr...
Abstract submission: influenzacentre.org//Centre_Acti...

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!

Nanopore's getting accurate, but

1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?

with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social

1 / N