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.
Kamila Szewczyk, Sven Rahmann: Hecate: A Modular Genomic Compressor https://arxiv.org/abs/2603.15390 https://arxiv.org/pdf/2603.15390 https://arxiv.org/html/2603.15390
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!
Fast Set Operations for Compact k-mer Sets https://www.biorxiv.org/content/10.64898/2026.05.24.727514v1