Jens Zentgraf

Deacon can now run in the browser using WebAssembly. Sequence data never leaves your machine. It currently supports FASTA/Q filtering using indexes up to 1GB in size.

Demo: bede.im/deacon

At the start of January, Johanna, @rorak.bsky.social and Sven traveled to Vancouver where Johanna presented our paper "Smaller and More Flexible Cuckoo Filters"(epubs.siam.org/doi/abs/10.1...) at the ALENEX 2026.
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🧬🖥️ Call for Abstracts OPEN!
Join us in celebrating 40 years of the German Conference on #Bioinformatics (#GCB2026) 🎉
📍 Saarbrücken | 🗓 22–25 Sep 2026
Submit your research & shape the future of Bioinformatics!

Deadlines
Workshops: 31 Mar 26
Talks: 3 May 26
Poster: 6 Aug 26

👉 GCB2026.DE

Cleanifier is a fast and memory-frugal tool to remove host contamination from microbial sequence data.
We build a pangenome gapped k-mer index using a probabilistic Cuckoo filter (
doi.org/10.48550/arX..., @Alenex 2026) for low memory requirements and fast queries.

Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index AbstractMotivation. The first step when working with DNA data of human-derived microbiomes is to remove human contamination for two reasons. First, many co

We are excited that our paper "Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index" is now published at Bioinformatics (doi.org/10.1093/bioi...).

You can find it at gitlab (gitlab.com/rahmannlab/c...) or install it via PyPI or Bioconda.

#RECOMB2026 will be in Thessaloniki, Greece on May 26-29, 2026. Satellites on May 24-25. Save the date!

Το συνέδριο #RECOMB2026 θα πραγματοποιηθεί στη Θεσσαλονίκη, στις 26-29 Μαΐου 2026. Οι δορυφορικές εκδηλώσεις θα διεξαχθούν στις 24-25 Μαΐου 2026. Σημειώστε την ημερομηνία!

Next year in march, the 2nd #Snakemake hackathon, this time at the #TUMunich in Germany, will take place. If you are interested in participating, follow the link on snakemake.github.io and check out the details!

Cleanifier: A fast and lightweight k-mer based tool to remove contamination in microbial sequence data https://www.biorxiv.org/content/10.1101/2025.06.24.661305v1

Excited to share that our preprint, Datavzrd: Rapid programming- and maintenance-free interactive visualization and communication of tabular data, is now up on bioRxiv! 🎉 #datavzrd

Datavzrd: Rapid programming- and maintenance-free interactive visualization and communication of tabular data https://www.biorxiv.org/content/10.1101/2025.04.03.647146v1