title: PhyResSE: a Web Tool Delineating Mycobacterium tuberculosis Antibiotic Resistance and Lineage from Whole-Genome Sequencing Data.
abstract: Antibiotic-resistant tuberculosis poses a global threat, causing the deaths of hundreds of thousands of people annually. While whole-genome sequencing (WGS), with its unprecedented level of detail, promises to play an increasingly important role in diagnosis, data analysis is a daunting challenge. Here, we present a simple-to-use web service (free for academic use at http://phyresse.org). Delineating both lineage and resistance, it provides state-of-the-art methodology to life scientists and physicians untrained in bioinformatics. It combines elaborate data processing and quality control, as befits human diagnostics, with a treasure trove of validated resistance data collected from well-characterized samples in-house and worldwide.
authors: Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany German Center for Infection Research (DZIF), Borstel Site, Borstel, Germany.
authors: Silke
authors: S
authors: Feuerriegel
authors: Bioinformatics, Research Center Borstel, Borstel, Germany.
authors: Viola
authors: V
authors: Schleusener
authors: Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany German Center for Infection Research (DZIF), Borstel Site, Borstel, Germany.
authors: Patrick
authors: P
authors: Beckert
authors: Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany.
authors: Thomas A
authors: TA
authors: Kohl
authors: Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy.
authors: Paolo
authors: P
authors: Miotto
authors: Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy.
authors: Daniela M
authors: DM
authors: Cirillo
authors: Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy.
authors: Andrea M
authors: AM
authors: Cabibbe
authors: Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany German Center for Infection Research (DZIF), Borstel Site, Borstel, Germany sniemann@fz-borstel.de kfellenberg@fz-borstel.de.
authors: Stefan
authors: S
authors: Niemann
authors: Bioinformatics, Research Center Borstel, Borstel, Germany sniemann@fz-borstel.de kfellenberg@fz-borstel.de.
authors: Kurt
authors: K
authors: Fellenberg
mesh_terms: D000995:Antitubercular Agents / Q000494:pharmacology; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000187:drug effects / Q000235:genetics; D012984:Software; D014376:Tuberculosis / Q000382:microbiology*
chemical_list: D000995:Antitubercular Agents