Malte Herold

💾 Prokka 1.15.6 is released!

This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics

github.com/tseemann/pro...

Ecosystem health shapes viral ecology in peatland soils - Nature Microbiology Metagenomics shows that viral diversity and community structure are shaped by geography and ecosystem health status, positioning viruses as unexpected players in peatland restoration.

Soil viruses are important regulators of ecosystem function, but what are their roles in environments that face long-term degradation and restoration? In our paper published today in Nature Micro, we asked how soil viruses influence peatland recovery, and vice versa. www.nature.com/articles/s41...

Hybridization between previously isolated lineages is main source of diversity within the population.

Hybridisation breaks species barriers in long-term coevolution of a cyanobacterial population.
buff.ly/EaJskBA

Easy and interactive taxonomic profiling with Metabuli App.
It integrates database curation, read QC, taxonomic profiling, and visualization right on your desktop.
No command line, server, or internet required.
Now published in Bioinformatics! 🧵1/5
doi.org/10.1093/bioi...
github.com/steineggerla...

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...
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Postdoctoral position - Uppsala University Postdoctoral position, Department of Immunology, Genetics and Pathology, Uppsala University

A postdoc position in genomics available at our infrastructure in Uppsala, Sweden! An interesting R&D role a bit outside the traditional academic environment, great colleagues, work at the forefront of (long-read) sequencing.

www.uu.se/en/about-uu/...

New Course – Live & Online
Tidyverse for Ecologists
June 16th–20th, 2025
Instructor: Dr. Gabriel Palma

This hands-on course covers ggplot2, dplyr, tidyr, and more.

#rstats #ecology #tidyverse #dataanalysis #openecology #rstatsforbiologists #dataviz

Full details:
www.prstats.org/course/tidyv...

Great job alert: ProPublica is hiring a computational journalist, "someone who will use technology and data to identify and unlock stories that would otherwise be out of reach."

Salary: $120K-$140K
Remote: ✅

Come join us!

BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata Bacteria are fascinating research objects in many disciplines for countless reasons, and whole-genome sequencing (WGS) has become the paramount methodology to advance our microbiological understanding...

Excited to share BakRep - our latest work published in
@MicrobioSoc
#MGen

>661,000 bacterial genomes, uniformly characterized & annotated, enriched with metadata, accessible via a flexible search engine:

doi.org/10.1099/mgen...

👇 1/7

Microbes are everywhere, but postdocs are hard to find: apply before the end of the month: vacatures.uva.nl/UvA/job/Post...

Metapresence: a tool for accurate species detection in metagenomics based on the genome-wide distribution of mapping reads | mSystems Despite the prevalent use of genome-centric alignment-based methods to characterize microbial community composition, there lacks a standardized approach for accurately identifying the species within a...

This work is a nice investigation of how the expected mathematical relationship between number of reads and breadth of coverage can inform "true" detection in metagenomes:
journals.asm.org/doi/10.1128/...

And on GitHub: github.com/davidesangui...

I've got a fully funded, 4-year PhD position available to work on virus-bacteria interactions in soils. Part of the GenerationResearch scheme at York aimed at widening access to postgrad research. Please share!
generationresearch.ac.uk/phd_proposal...

Hi everyone,
I am happy to share that a permanent data scientist position is very likely to be opened in our group.

We're looking for people interested in working with statistics and computers in a wide variety of research questions in genetics.

The application process will be at jobs.inrae.fr

isn't secondary==no included in the short-read preset?

Ryan Wick has tested out the latest kits and basecalling for bacterial genome assembly:

rrwick.github.io/2023/10/24/o...

At assembly error rates like this I start to begin wondering what is "ground truth"