BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology.

Biological Sciences Research Methodologies Microbiology Sequence Analysis

Journal

iScience
ISSN: 2589-0042
Titre abrégé: iScience
Pays: United States
ID NLM: 101724038

Informations de publication

Date de publication:
24 Jan 2020
Historique:
received: 03 06 2019
revised: 21 10 2019
accepted: 09 12 2019
pubmed: 31 12 2019
medline: 31 12 2019
entrez: 31 12 2019
Statut: ppublish

Résumé

Despite rapid advances in whole genome sequencing (WGS) technologies, their integration into routine microbiological diagnostics has been hampered by the lack of standardized downstream bioinformatics analysis. We developed a comprehensive and computationally low-resource bioinformatics pipeline (BacPipe) enabling direct analyses of bacterial whole-genome sequences (raw reads or contigs) obtained from second- or third-generation sequencing technologies. A graphical user interface was developed to visualize real-time progression of the analysis. The scalability and speed of BacPipe in handling large datasets was demonstrated using 4,139 Illumina paired-end sequence files of publicly available bacterial genomes (2.9-5.4 Mb) from the European Nucleotide Archive. BacPipe is integrated in EBI-SELECTA, a project-specific portal (H2020-COMPARE), and is available as an independent docker image that can be used across Windows- and Unix-based systems. BacPipe offers a fully automated "one-stop" bacterial WGS analysis pipeline to overcome the major hurdle of WGS data analysis in hospitals and public-health and for infection control monitoring.

Identifiants

DOI: 10.1016/j.isci.2019.100769 PMID: 31887656 PMC: PMC6941874
pubmed: 31887656
pii: S2589-0042(19)30514-0
doi: 10.1016/j.isci.2019.100769
pmc: PMC6941874
pii:
doi:

Types de publication

Journal Article

Langues

eng

Pagination

100769

Informations de copyright

Copyright © 2019 The Author(s). Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of Interests None declared.

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Auteurs

Basil B Xavier (BB)

Laboratory of Medical Microbiology, Campus Drie Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp 2610, Belgium.

Mohamed Mysara (M)

Laboratory of Medical Microbiology, Campus Drie Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp 2610, Belgium; Microbiology Unit, Belgian Nuclear Research Center (SCK•CEN), Mol 2400, Belgium.

Mattia Bolzan (M)

Laboratory of Medical Microbiology, Campus Drie Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610 Wilrijk, Belgium.

Bruno Ribeiro-Gonçalves (B)

Instituto de Microbiologia and Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, Lisboa 1649-028, Portugal.

Blaise T F Alako (BTF)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK.

Peter Harrison (P)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK.

Christine Lammens (C)

Laboratory of Medical Microbiology, Campus Drie Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp 2610, Belgium.

Samir Kumar-Singh (S)

Laboratory of Medical Microbiology, Campus Drie Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Molecular Pathology Group, Cell Biology and Histology, University of Antwerp, Antwerp 2610, Belgium.

Herman Goossens (H)

Laboratory of Medical Microbiology, Campus Drie Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp 2610, Belgium.

João A Carriço (JA)

Instituto de Microbiologia and Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, Lisboa 1649-028, Portugal.

Guy Cochrane (G)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK.

Surbhi Malhotra-Kumar (S)

Laboratory of Medical Microbiology, Campus Drie Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp 2610, Belgium. Electronic address: surbhi.malhotra@uantwerpen.be.

Classifications MeSH