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BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology
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 (Ba...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6941874/ https://www.ncbi.nlm.nih.gov/pubmed/31887656 http://dx.doi.org/10.1016/j.isci.2019.100769 |
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author | Xavier, Basil B. Mysara, Mohamed Bolzan, Mattia Ribeiro-Gonçalves, Bruno Alako, Blaise T.F. Harrison, Peter Lammens, Christine Kumar-Singh, Samir Goossens, Herman Carriço, João A. Cochrane, Guy Malhotra-Kumar, Surbhi |
author_facet | Xavier, Basil B. Mysara, Mohamed Bolzan, Mattia Ribeiro-Gonçalves, Bruno Alako, Blaise T.F. Harrison, Peter Lammens, Christine Kumar-Singh, Samir Goossens, Herman Carriço, João A. Cochrane, Guy Malhotra-Kumar, Surbhi |
author_sort | Xavier, Basil B. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6941874 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-69418742020-01-06 BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology Xavier, Basil B. Mysara, Mohamed Bolzan, Mattia Ribeiro-Gonçalves, Bruno Alako, Blaise T.F. Harrison, Peter Lammens, Christine Kumar-Singh, Samir Goossens, Herman Carriço, João A. Cochrane, Guy Malhotra-Kumar, Surbhi iScience Article 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. Elsevier 2019-12-12 /pmc/articles/PMC6941874/ /pubmed/31887656 http://dx.doi.org/10.1016/j.isci.2019.100769 Text en © 2019 The Author(s) http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Article Xavier, Basil B. Mysara, Mohamed Bolzan, Mattia Ribeiro-Gonçalves, Bruno Alako, Blaise T.F. Harrison, Peter Lammens, Christine Kumar-Singh, Samir Goossens, Herman Carriço, João A. Cochrane, Guy Malhotra-Kumar, Surbhi BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology |
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 |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6941874/ https://www.ncbi.nlm.nih.gov/pubmed/31887656 http://dx.doi.org/10.1016/j.isci.2019.100769 |
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