BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology
Summary: 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 pip...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2020-01-01
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| Series: | iScience |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004219305140 |
| _version_ | 1819237417363701760 |
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| author | Basil B. Xavier Mohamed Mysara Mattia Bolzan Bruno Ribeiro-Gonçalves Blaise T.F. Alako Peter Harrison Christine Lammens Samir Kumar-Singh Herman Goossens João A. Carriço Guy Cochrane Surbhi Malhotra-Kumar |
| author_facet | Basil B. Xavier Mohamed Mysara Mattia Bolzan Bruno Ribeiro-Gonçalves Blaise T.F. Alako Peter Harrison Christine Lammens Samir Kumar-Singh Herman Goossens João A. Carriço Guy Cochrane Surbhi Malhotra-Kumar |
| author_sort | Basil B. Xavier |
| collection | DOAJ |
| description | Summary: 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. : Biological Sciences Research Methodologies; Microbiology; Sequence Analysis Subject Areas: Biological Sciences Research Methodologies, Microbiology, Sequence Analysis |
| first_indexed | 2024-12-23T13:20:00Z |
| format | Article |
| id | doaj.art-744c6e15e0f04c218039ac9a13ae02f3 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-12-23T13:20:00Z |
| publishDate | 2020-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-744c6e15e0f04c218039ac9a13ae02f32022-12-21T17:45:29ZengElsevieriScience2589-00422020-01-01231BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic BacteriologyBasil B. Xavier0Mohamed Mysara1Mattia Bolzan2Bruno Ribeiro-Gonçalves3Blaise T.F. Alako4Peter Harrison5Christine Lammens6Samir Kumar-Singh7Herman Goossens8João A. Carriço9Guy Cochrane10Surbhi Malhotra-Kumar11Laboratory 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, BelgiumLaboratory 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, BelgiumLaboratory of Medical Microbiology, Campus Drie Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610 Wilrijk, BelgiumInstituto de Microbiologia and Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, Lisboa 1649-028, PortugalEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UKEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UKLaboratory 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, BelgiumLaboratory 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, BelgiumLaboratory 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, BelgiumInstituto de Microbiologia and Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, Lisboa 1649-028, PortugalEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UKLaboratory 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; Corresponding authorSummary: 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. : Biological Sciences Research Methodologies; Microbiology; Sequence Analysis Subject Areas: Biological Sciences Research Methodologies, Microbiology, Sequence Analysishttp://www.sciencedirect.com/science/article/pii/S2589004219305140 |
| spellingShingle | Basil B. Xavier Mohamed Mysara Mattia Bolzan Bruno Ribeiro-Gonçalves Blaise T.F. Alako Peter Harrison Christine Lammens Samir Kumar-Singh Herman Goossens João A. Carriço Guy Cochrane Surbhi Malhotra-Kumar BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology iScience |
| title | BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology |
| title_full | BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology |
| title_fullStr | BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology |
| title_full_unstemmed | BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology |
| title_short | BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology |
| title_sort | bacpipe a rapid user friendly whole genome sequencing pipeline for clinical diagnostic bacteriology |
| url | http://www.sciencedirect.com/science/article/pii/S2589004219305140 |
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