ArticleiScience2020
BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology.
Article in iScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 48 citations in OpenAlex.
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- Application of next-generation sequencing to investigate a Serratia marcescens outbreak in a neonatal intensive care unit.Antimicrobial resistance and infection control · 2026Article
- Characterization of genome-wide transpositions induced by colistin exposure in multi-drug-resistantAntimicrobial agents and chemotherapy · 2025Article
- Pneumococcal genotype 23B1 as a driver of increased 23B serotype carriage, penicillin non-susceptibility, and invasive disease in Belgium: a retrospective analysis.Journal of clinical microbiology · 2025Article
- BacExplorer: an integrated platform forBioinformatics advances · 2025Article
- Tracing carriage, acquisition, and transmission of ESBL-producing Escherichia coli over two years in a tertiary care hospital.Genome medicine · 2024Observational
- Genomic Investigation and Comparative Analysis of European High-Risk Clone ofMicroorganisms · 2024Article
- Genomic epidemiological analysis of a single-centre polyclonal outbreak ofEuro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2024Article
- The Association between Resistance and Virulence ofMicroorganisms · 2024Article
- A microbiological and genomic perspective of globally collected Escherichia coli from adults hospitalized with invasive E. coli disease.The Journal of antimicrobial chemotherapy · 2024Observational
- The GEA pipeline for characterizing Escherichia coli and Salmonella genomes.Scientific reports · 2024Article
- Assessment of three antibiotic combination regimens against Gram-negative bacteria causing neonatal sepsis in low- and middle-income countries.Nature communications · 2024Article
- High-resolution genomics identifies pneumococcal diversity and persistence of vaccine types in children with community-acquired pneumonia in the UK and Ireland.BMC microbiology · 2024Article
- Assessment of Colistin Heteroresistance among Multidrug-ResistantAntibiotics (Basel, Switzerland) · 2024Article
- Role of transcriptomic and genomic analyses in improving the comprehension of cefiderocol activity inmSphere · 2024Article
- One Health surveillance of colistin-resistant Enterobacterales in Belgium and the Netherlands between 2017 and 2019.PloS one · 2024Article
- Virulence attributes of successful methicillin-resistantClinical microbiology reviews · 2023Review
- MIST: A microbial identification and source tracking system for next-generation sequencing data.iMeta · 2023Article
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.