PathoFact 2.0: an integrative pipeline for the prediction of antimicrobial resistance genes, virulence factors, toxins and toxin-associated proteins, and biosynthetic gene clusters in metagenomes [* Cross-Reference *]

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Luis F Delgado; Júlia Ortís Sunyer; Cedric C Laczny; Oskar Hickl; Patrick May; Paul Wilmes, 2026, "PathoFact 2.0: an integrative pipeline for the prediction of antimicrobial resistance genes, virulence factors, toxins and toxin-associated proteins, and biosynthetic gene clusters in metagenomes [* Cross-Reference *]", https://lore.list.lu/citation?persistentId=perma:LIST.UAXFWP, LIST Open Repository, V1
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Description
Background: Antimicrobial resistance genes (ARGs) and virulence factors (VFs) are central contributors to the global health crisis surrounding drug-resistant infections. Findings: We introduce PathoFact 2.0, an enhanced pipeline for improved ARG, VF, toxin, and biosynthetic gene clusters (BGCs) prediction. Key improvements include an updated machine learning (ML) model for VF identification, expanded hidden Markov model profiles for VFs and toxin-associated proteins, a new ML model for toxin and toxin-associated proteins identification, and the integration of antiSMASH 7.0 for predicting BGCs. Conclusions: Our upgrades make PathoFact 2.0 a more powerful and user-friendly platform for predicting microbiome-based pathogenicity and resistance, providing a crucial tool for better understanding and addressing the challenges posed by antimicrobial resistance and infectious diseases. PathoFact 2.0 is available at https://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2. It is compatible with Linux operating systems. (2026-01-01)
***This entry has been automatically imported via OpenAlex by LIST harvest scripts. Please refer to https://doi.org/10.1093/gigascience/giag062 for the original and latest version of the publication*** (2026-07-01)
Subject Chemistry; Computer and Information Science; Medicine, Health and Life Sciences; Physics
Keyword Pipeline (software), Virulence, Gene, Antibiotic resistance, Pathogenicity, Key (lock), Antimicrobial, Gene cluster
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