biostudies-literatureUnknown7(3)Seidel JPrivacy is paramount in health data, particularly in human genetics, where information extends beyond individuals to their relatives. Metagenomic datasets contain substantial human genetic material, necessitating careful handling to mitigate data leakage risks when sharing or publishing. The same applies to genetic datasets from the environment or datasets from contaminated laboratory samples, although to a lesser extent. Completely removing human sequence data while retaining unbiased nonhuman reads is not achievable currently, but several tools exist. To address these topics, we developed nf-core/detaxizer, a nextflow-based pipeline that employs Kraken2 and bbmap/bbduk for taxonomic classification, identifying and optionally filtering <i>Homo sapiens</i> reads. Due to its generalized desNAR genomics and bioinformaticslqaf125https://www.ebi.ac.uk/biostudies/studies/S-EPMC12455401biostudies-literaturenf-core/detaxizer: a benchmarking study for decontamination from human sequences.PMC12455401Kaipf CSeidel JStraub DNahnsen Sfalsenf-core/detaxizer: a benchmarking study for decontamination from human sequences.Privacy is paramount in health data, particularly in human genetics, where information extends beyond individuals to their relatives. Metagenomic datasets contain substantial human genetic material, necessitating careful handling to mitigate data leakage risks when sharing or publishing. The same applies to genetic datasets from the environment or datasets from contaminated laboratory samples, although to a lesser extent. Completely removing human sequence data while retaining unbiased nonhuman reads is not achievable currently, but several tools exist. To address these topics, we developed nf-core/detaxizer, a nextflow-based pipeline that employs Kraken2 and bbmap/bbduk for taxonomic classification, identifying and optionally filtering <i>Homo sapiens</i> reads. Due to its generalized des2025-01-01T00:00:00Z2025 Sep2026-05-01T03:15:51.218Z2026-05-01T03:10:02.742ZS-EPMC124554014099556610.1093/nargab/lqaf125