Cited 15 times since 2020 (3.9 per year) source: EuropePMC Bioinformatics (Oxford, England), Volume 36, Issue 12, 1 1 2020, Pages 3874-3876 gplas: a comprehensive tool for plasmid analysis using short-read graphs. Arredondo-Alonso S, Bootsma M, Hein Y, Rogers MRC, Corander J, Willems RJL, Schürch AC

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.

Bioinformatics. 2020 6;36(12):3874-3876