ArticleBMC genomics2021
MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction.
Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Nanopore Sequencing for Chikungunya Virus: Principles and Application.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Whole genome sequencing analysis and functional characterization of Lacticaseibacillus rhamnosus HP-B1083.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- PaVarDB: a database and web platform for missense variant analysis in Pseudomonas aeruginosa using an end-to-end BVbase pipeline.Database : the journal of biological databases and curation · 2026Article
- PUDU (pipeline for universal diversity unveiling): an accessible end-to-end workflow for taxonomic profiling and ecological visualization of environmental microbiomes across amplicon, shotgun, and long-read sequencing.Frontiers in bioinformatics · 2026Article
- Global population structure of Shiga toxin-producingMicrobial genomics · 2026Article
- Article
- Complete genome sequence ofMicrobiology resource announcements · 2025Article
- Genome size estimation from long read overlaps.Bioinformatics (Oxford, England) · 2025Article
- Complete genome sequences ofMicrobiology resource announcements · 2025Article
- Antigenic variation is caused by long plasmid segment conversion in a hard tick-borne relapsing fever Borrelia miyamotoi.PLoS pathogens · 2025Article
- Prevalence, sequence diversity, and amplification of an IS-associated enterotoxin gene,Frontiers in microbiology · 2025Article
- Genome Assembly, Polishing, and Analysis of the Chytrid Batrachochytrium salamandrivorans.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Comprehensive Safety Assessment ofCurrent issues in molecular biology · 2024Article
- Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies.Microbial genomics · 2024Article
- High-riskeLife · 2024Article
- Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies.bioRxiv : the preprint server for biology · 2024Article
- Complete genome sequences of 11Microbiology resource announcements · 2024Article
- Molecular characterization of an outbreak-involved Bacillus anthracis strain confirms the spillover of anthrax from West Africa.Infectious diseases of poverty · 2024Article
- Comparative genomics of symbioticMicrobial genomics · 2023Article
- Illuminating the Genomic Landscape ofMicroorganisms · 2023Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOxford Nanopore Technology (ONT) long-read sequencing has become a popular platform for microbial researchers due to the accessibility and affordability of its devices. However, easy and automated construction of high-quality bacterial genomes using nanopore reads remains challenging. Here we aimed to create a reproducible end-to-end bacterial genome assembly pipeline using ONT in combination with Illumina sequencing.
resultsWe evaluated the performance of several popular tools used during genome reconstruction, including base-calling, filtering, assembly, and polishing. We also assessed overall genome accuracy using ONT both natively and with Illumina. All steps were validated using the high-quality complete reference genome for the Escherichia coli sequence type (ST)131 strain EC958. Software chosen at each stage were incorporated into our final pipeline, MicroPIPE. Further validation of MicroPIPE was carried out using 11 additional ST131 E. coli isolates, which demonstrated that complete circularised chromosomes and plasmids could be achieved without manual intervention. Twelve publicly available Gram-negative and Gram-positive bacterial genomes (with available raw ONT data and matched complete genomes) were also assembled using MicroPIPE. We found that revised basecalling and updated assembly of the majority of these genomes resulted in improved accuracy compared to the current publicly available complete genomes.
conclusionsMicroPIPE is built in modules using Singularity container images and the bioinformatics workflow manager Nextflow, allowing changes and adjustments to be made in response to future tool development. Overall, MicroPIPE provides an easy-access, end-to-end solution for attaining high-quality bacterial genomes. MicroPIPE is available at https://github.com/BeatsonLab-MicrobialGenomics/micropipe .
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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.