Jana Batovska

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

Autocycler: long-read consensus assembly for bacterial genomes AbstractMotivation. Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-l

Happy to share that the paper describing Autocycler is now 100% up:
doi.org/10.1093/bioi...
(1/3)

X-Mapper 🦠🧬🧪 - a sequence aligner developed for microbes, now on Bioconda! 🚀
• 11–24× fewer suboptimal alignments (same for human genome)
• 3–579× lower inconsistency
• improves on ~30% of reads aligned to non-target species
github.com/mathjeff/map...
bioconda.github.io/recipes/x-ma...
#microsky

A fast, accurate ‘sequence search engine’ The MetaGraph tool can search through millions of published DNA, RNA and protein records in a matter of seconds. Developed by SIB scientists at ETH Zurich, the tool overcomes current limitations in an...

🔎 Check out MetaGraph – a powerful search engine for DNA, RNA and protein sequences in large public repositories. This important milestone in computational genomics was published in Nature, by SIB scientists at ETH Zurich.

Surveying Tropical Faunal Diversity via Airborne DNA Analyses Here, we assess the potential of airborne eDNA (airDNA) metabarcoding to characterize arthropod and vertebrate assemblages in a tropical forest. We deployed 28 high-flow air samplers across a 1.5 km2…

You can't just pull data out of thin air. Or can you...?
That's exactly what Craine et al. did in Panama, through air sampling and airDNA metabarcoding, detecting ~1800 arthropod and vertebrate OTUs.
www.biorxiv.org/content/10.1...
#nanopore #airsampling #metabarcoding #biodiversity

Webinar: Squiggles to the Rescue: Nanopore Sequencing and AI for Rapid One Health Surveillance

Join us as Dr. Lara Urban explores how nanopore sequencing and AI can empower rapid One Health strategies.

Thursday, Oct. 23, 2025, 11:00 AM PT

Register Now: www.zymoresearch.com/pages/squigg...

The new -outfmt 20 in BLAST 😍. No more frustrated googling to remember which column is which.....

🥰

#MicroSeq2025

Until next year, @mozztacular.bsky.social, Asad, @royalfizzbin.bsky.social, Mozammel, @wytamma.bsky.social , Bec, and @rhyshparry.bsky.social out!
#MicroSeq2025

And that’s a wrap of #MicroSeq2025! A huge thanks to all our brilliant presenters, fantastic chairs, and wonderfully engaged audience. We hope you all enjoyed the conference as much as we did, and can’t wait to see you next year at #MicroSeq2026!

What a fantastic way to wrap up our #MicroSeq2025 talks! Leah gives our junior researchers some valuable career advice, like go new places, find mentors, reflect and introspect, and be strategic about taking opportunities!

🐖Manavi Muralidhar evaluates #metagenomics as an early pathogen detection method in piggery wastewater samples. Explore the ways metagenomics can monitor disease outbreaks and how to improve sensitivity for successful implementation! #MicroSeq2025 #OneHealth #wastewater

💾 @himal2007.bsky.social introduces mlstdb, which handles authentication and automates Multi-Locus Sequence Typing scheme downloads from major repositories amidst ongoing data accessibility challenges. “Always Be Validating” - great motto! #MicroSeq2025 #MLST #bioinformatics #databases

Some more incredibly valuable advice from Jackie: refine experimental designs, be critical of bioinformatic output, and perhaps most importantly, name your novel viruses something that brings you joy! Like Jackie’s coolest virus name: Lilsebastian narna-like virus.

GitHub - ausbiopathgenDB/AustralianBiosecurityGenomicDatabase: A genomic reference sequence database for notifiable animal disease pathogens in Australia. A genomic reference sequence database for notifiable animal disease pathogens in Australia. - ausbiopathgenDB/AustralianBiosecurityGenomicDatabase

github.com/ausbiopathge...

Extract > library prep > sequencing > so much data! This results in a critical need for specifically curated genomic databases to streamline data analysis for viral surveillance and pathogen monitoring. Can't be missing notifiable diseases in your data sets! #MicroSeq2025

Your #MicroSeq2025 committee - @mozztacular.bsky.social , Asad Prodhan, @royalfizzbin.bsky.social , Mozammel Hoque, @wytamma.bsky.social , Rebecca Roach, and @rhyshparry.bsky.social - are all here and ready to go! 🫡

Please feel free to reach out to any of us w/ questions or concerns at any time ♥️

YouTube video by Institut Pasteur La dengue aux commandes

Does #dengue virus hijack #mosquitoes' brain? Study led by Felix Hol @pasteur.fr discovered that infected mosquitoes take smaller blood meals. As a result, they bite more often, and potentially infect infect more people.

(video in French with English subtitles available)
youtu.be/2u_qckfAQa4?...

a promo image showing various pages from the book, each page showcasing different animals like an orchid mantis, opabinia, a butterfly. the art featured shows a range of different medium, including digital, plushie, papercraft, 3D render, comic, and so on.

We present: The Art of #InverteFest - August 2025 Edition
A digital art book showcasing the work of 100 artists from around the world, in celebration of overlooked invertebrate fauna.

Thank you to the artists who contributed to our book!

Download here drive.google.com/file/d/19wfG...

#Art #SciArt

Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1
www.medrxiv.org/content/10.1...

Photograph of Dr Jackie Mahar, a researcher based at Agriculture Victoria Research. Her portrait is decorated with cartoons of microbes. Dr Jackie Mahar is an invited plenary speaker for MicroSeq2025.

✨ #MicroSeq2025 Plenary Highlight! ✨
Dr Jackie Mahar is an evolutionary virologist & bioinformatician based at CSIRO, managing projects on NGS-based phylogenomics of zoonotic & animal viruses for pathogen discovery, surveillance & viral ecology.
Register👇
trybooking.com/events/landing/1424679

CoverM: Read alignment statistics for metagenomics AbstractSummary. Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating r

CoverM is published!

CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs

Virus 'previously exotic to Australia' found in Tasmanian potatoes Mop-top potato virus, which does not harm humans, has been found in multiple potatoes on a Tasmanian farm — a first for Australia.

Mop-top potato virus, which does not harm humans, has been found in multiple potatoes on a Tasmanian farm — a first for Australia.

Growth of public metagenomes over time

A 1.0 release for Sandpiper. 700,000 microbial community profiles (3x the last version, 4.7 Pbp metaG), searchable via the @ace-gtdb.bsky.social R226 taxonomy that just dropped. MetaGs are going exponential, but we are still nowhere near a MAG for all species. sandpiper.qut.edu.au #microsky 🧬🖥️ 1/2

Our high-precision metagenomic strain caller, PHLAME, is now published in Cell Reports!! www.cell.com/cell-reports...

PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.

Rapid species-level metagenome profiling and containment estimation with sylph - Nature Biotechnology The microbial composition of metagenomes is identified in seconds by profiling against large databases.

The microbial composition of metagenomes is identified in seconds by profiling against large databases go.nature.com/3BBVqDC
rdcu.be/eCbj4

(Harvard STAT115): Introduction to Bioinformatics and Computational Biology by Shirley Liu.
liulab-dfci.github.io/bioinfo-com...

A new long-read metagenome assembler has been released: myloasm. Very exciting! Looking forward to trying it out.