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Title
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BacPipe : a rapid, user-friendly whole-genome sequencing pipeline for clinical diagnostic bacteriology
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Author
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Abstract
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| 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. |
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Language
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English
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Source (journal)
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iScience
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Publication
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Elsevier
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2020
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ISSN
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2589-0042
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DOI
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10.1016/J.ISCI.2019.100769
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Volume/pages
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23
:1
(2020)
, 28 p.
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Article Reference
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100769
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ISI
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000508685200021
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Pubmed ID
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31887656
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Medium
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E-only publicatie
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Full text (Publisher's DOI)
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Full text (open access)
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