Dataset Information
Gplas: a comprehensive tool for plasmid analysis using short-read graphs.
Ontology highlight
ABSTRACT: Summary
Plasmids 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.
SUBMITTER: Arredondo-Alonso S
PROVIDER: S-EPMC7320608 | biostudies-literature | 2020 Jun
REPOSITORIES: biostudies-literature
Publications
gplas: a comprehensive tool for plasmid analysis using short-read graphs.
Bioinformatics (Oxford, England) 20200601 12
<h4>Summary</h4>Plasmids 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 c ...[more]