ArticleBioinformatics (Oxford, England)2020
gplas: a comprehensive tool for plasmid analysis using short-read graphs.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 36 citations in OpenAlex.
- gplasCC: classification and recovery of plasmids from short-read sequencing data for any bacterial species.NAR genomics and bioinformatics · 2026Article
- ProFiT-SPEci-FISH: a novel approach for linking plasmids to hosts in complex microbial communities at the single-cell level.Microbiome · 2025Article
- Plaseval: a framework for comparing and evaluating plasmid detection tools.BMC bioinformatics · 2024Article
- PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids inMicrobial genomics · 2024Article
- Local and Environmental Reservoirs ofGeoHealth · 2023Article
- Mge-cluster: a reference-free approach for typing bacterial plasmids.NAR genomics and bioinformatics · 2023Article
- PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer.Nucleic acids research · 2023Article
- PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning.Bioinformatics (Oxford, England) · 2023Article
- Taking hospital pathogen surveillance to the next level.Microbial genomics · 2023Article
- plASgraph2: using graph neural networks to detect plasmid contigs from an assembly graph.Frontiers in microbiology · 2023Article
- Characterization of qnrB-carrying plasmids from ESBL- and non-ESBL-producing Escherichia coli.BMC genomics · 2022Article
- The Space-Exposed Kombucha Microbial Community MemberFrontiers in microbiology · 2022Article
- RecoveringMicroorganisms · 2021Article
- SCAPP: an algorithm for improved plasmid assembly in metagenomes.Microbiome · 2021Article
- Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals.Genome medicine · 2021Article
- Molecular Characterization and Survive Abilities ofFrontiers in microbiology · 2021Article
- Metagenomic Data Assembly - The Way of Decoding Unknown Microorganisms.Frontiers in microbiology · 2021Review
- The role of mobile genetic elements in organic micropollutant degradation during biological wastewater treatment.Water research X · 2020Review
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryPlasmids can horizontally transmit genetic traits, enabling rapid bacterial adaptation to new environments and hosts. Short-read whole-genome sequencing data are often applied to large-scale bacterial comparative genomics projects but the reconstruction of plasmids from these data is facing severe limitations, such as the inability to distinguish plasmids from each other in a bacterial genome. We developed gplas, a new approach to reliably separate plasmid contigs into discrete components using sequence composition, coverage, assembly graph information and network partitioning based on a pruned network of plasmid unitigs. Gplas facilitates the analysis of large numbers of bacterial isolates and allows a detailed analysis of plasmid epidemiology based solely on short-read sequence data. AVAILABILITY AND IMPLEMENTATION: Gplas is written in R, Bash and uses a Snakemake pipeline as a workflow management system. Gplas is available under the GNU General Public License v3.0 at https://gitlab.com/sirarredondo/gplas.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.