Publication
Title
BacPipe : a rapid, user-friendly whole-genome sequencing pipeline for clinical diagnostic bacteriology
Author
Abstract
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.
Language
English
Source (journal)
iScience
Publication
Elsevier , 2020
ISSN
2589-0042
Volume/pages
23 :1 (2020) , 28 p.
Article Reference
100769
ISI
000508685200021
Pubmed ID
31887656
Medium
E-only publicatie
Full text (Publisher's DOI)
Full text (open access)
UAntwerpen
Faculty/Department
Research group
Project info
COllaborative Management Platform for detection and Analyses of (Re-)emerging and foodborne outbreaks in Europe (COMPARE) ua_31563
Combatting bacterial resistance in Europe (COMBACTE-NET). ua_28586
Publication type
Subject
Affiliation
Publications with a UAntwerp address
External links
Web of Science
Record
Identifier
Creation 13.02.2020
Last edited 15.11.2022
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