Martin Hölzer

Genomics, Bioinformatics, Nextflow, Scout. Tweets are my own. Researcher @rki_de.

[Martin Hölzer @martinhoelzer]

🚀 New release of our ONT methylation Nextflow pipeline!

Developed by my PhD student Valentina at RKI’s Genome Competence Center 🧬

🔧 Updates:

- Updated Modkit envs
- Auto-thresholding for confidence
- Improved README

Check it out 👇
🔗 https://t.co/hZkiyWyFW8

[Martin Hölzer @martinhoelzer]

New paper out! 🧬

With my PhD student Valentina, we supported a study led by FLI (Jena) on ONT genome assemblies of pathogenic bacteria.

We investigated methylation-linked basecalling errors — 6.5% of errors tied to methylation!

🔗 https://t.co/Pm0neMUBWZ

[Martin Hölzer @martinhoelzer]

🌍🧬 We’re hiring a Scientist (Bioinformatics) to work at the intersection of PH & genomics. The role bridges our Center for International Health Protection & Genome Competence Center in the “Health Security Partnership for Africa” project.
🔗 Apply 31 Aug https://t.co/w7EYsZj9dS

[Martin Hölzer @martinhoelzer]

🚨 New paper out!

Targeted decontamination of sequencing data with CLEAN

🧬 Remove spike-ins, host DNA, rRNA & more
✅ Works with Illumina & Nanopore
🔁 Reproducible & open-source

📄 https://t.co/egHifgo61K
💻 https://t.co/PE8GhPtS5v

Clean it, dammit!

[Martin Hölzer @martinhoelzer]

Happy the LaTeX template I created for DFG proposals is being used! 🎉
Just heard from someone in data engineering who got funded using it (🎯 content matters most, but hey, layout helps too 😄)

See: https://t.co/jB4t1bodb8

Also loving the community input via PRs & issues! 💙

[Martin Hölzer @martinhoelzer]

Just out: our new paper on NGS analysis in Greek patients with predominantly antibody deficiencies! 🇬🇷🔬

A great collaboration that began when first author Achilleas joined my team via Erasmus 🇪🇺 — now I’m thrilled to be on his PhD committee.

👉 https://t.co/WeEANlcfbX

[Martin Hölzer @martinhoelzer]

🚨 New in Nature Communications!

CoVerage (https://t.co/opeGJjLsEC) enables early in silico detection of emerging SARS-CoV-2 variants.

Led by Helmholtz Centre for Infection Research, driving innovation in genomic surveillance.

🔗 https://t.co/MgGCrFQZZR

#GenomicSurveillance

[Martin Hölzer @martinhoelzer]

🚀 We've updated our diff gene expression analysis pipeline – including the latest SortMeRNA for improved rRNA removal!

This also resolves recent bugs reported by users.

🔬 Looking for a reproducible & comprehensive transcriptome analysis pipeline?
👉 https://t.co/gyPlFluk7O

[Martin Hölzer @martinhoelzer]

🚨 Preprint!

We've adapted SC2 wastewater surv to track the 2022 #mpox outbreak in Germany using a novel NGS panel 🧪

✅ 90% MPXV genome coverage
🧬 Specific mutations
📍 Wastewater = stigma-free surveillance

Led by - @Lackner_TUDa, check it out:
🔗 https://t.co/J6jqrhX0cN

[Ryan Wick @rrwick]

New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: https://t.co/NksiyESF7u
(1/5)

[Martin Hölzer @martinhoelzer]

@phiweger Journal latest after acceptance: so, now please convert everything to Word. 🤷

[Martin Hölzer @martinhoelzer]

My little POCP (percentage of conserved proteins) @nextflowio pipeline now also plots the results in a heatmap. Here are five Chlamydia strains, for example.

I hope it's useful for some!

Code: https://t.co/e3Ydc5fJFu

[Zamin Iqbal @ZaminIqbal]

I'm going to be advertising a PhD studentship (open to international students) working on long read pangenome / assembly algorithms in bacteria. Would suit someone with maths/compsci background. Aptitude and interest more important than experience. Advert to follow. Pls RT!

[Martin Hölzer @martinhoelzer]

We attended the International #OneHealth Symposium in Berlin and the team presented our research @rki_de in pangenomics, panproteomics, DNA modifications, @nanopore, and wastewater surveillance for AMR detection. Thanks to the great team, all collaborators, and organizers!

[Robert Koch-Institut @rki_de]

🇯🇵🇩🇪 Kitasato-Koch-Symposium: Deutsch-japanischer Wissenschaftsaustausch seit 1886.
Im September wurde beim 16. Symposium in Berlin über Themen wie Abwassermonitoring, Bioinformatik und Antibiotikaresistenz diskutiert.

Mehr Einblicke:
📹https://t.co/ePVQLyOzJL

@KitasatoUniv

[Martin Hölzer @martinhoelzer]

@Friedemann1 Awesome! Congratz!

It's really great that the data is presented in this way to encourage follow-up research.

I also feel a bit reminded of the old days when we had this (very basic!) "interactive gene viewer" ;)

https://t.co/QfE4m5ipxj

[Paul Gardner @ppgardne]

A little backstory for: "A Bioinformatician, Computer Scientist, and Geneticist lead bioinformatic tool development - which one is better?" https://t.co/oT2IFJ0EU2 #1/9

[Martin Hölzer @martinhoelzer]

@daanspeth Really cool, thanks!

Do you know how easy it is to create a database for kraken2 based on your files? I saw that you also provide a taxonomy file. We might give that a try...

[Emanuel Wyler @ewyler]

Out now: our collaborative effort on "Pathogen dynamics and discovery of novel viruses and enzymes by deep nucleic acid sequencing of wastewater"
https://t.co/LXoLUdE0Uk – with >100 total RNA/DNA sequencings over 17 months from a Berlin wastewater plant. Summary below … (1/10)

[Martin Hölzer @martinhoelzer]

@vvenki22 @maxplanckpress Now it's accessible ;)

[Martin Hölzer @martinhoelzer]

@vvenki22 @maxplanckpress Yeah, it seems the page is not (yet) publicly accessible