Journal
ISCIENCE
Volume 23, Issue 1, Pages -Publisher
CELL PRESS
DOI: 10.1016/j.isci.2019.100769
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Funding
- European Union Horizon 2020 Research and Innovation Programme: Compare (COllaborative Management Platform for detection and Analyses of (Re-)) [643476]
- Innovative Medicines Initiative Joint Undertaking [~ 115523]
- European Union
- (EFPIA companies in kind contribution) [Tubitak/0004/2014]
- Fundacao para a Ciencia e a Tecnologia (FCT)/Scientific and Technological Research Council of Turkey(TUBITAK)
- Oneida project [LISBOA-01-0145-Feder-016417]
- FCT National Funds
- Fundacao para a ciencia e a technologia [PSFRH/BD/101448/2014]
- Fundação para a Ciência e a Tecnologia [TUBITAK/0004/2014] Funding Source: FCT
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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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