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bioRxiv · 10.1101/835900

gplas: a comprehensive tool for plasmid analysis using short-read graphs

Arredondo-Alonso, S.·Bootsma, M.·Hein, Y.·Rogers, M. R. C.·Corander, J.·Willems, R. J.·Schürch, A. C.
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Abstract

SummaryPlasmids can horizontally transmit genetic traits, enabling rapid bacterial adaptation to new environments and hosts. Short-read whole-genome sequencing data is 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 clustering 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.\n\nAvailability and implementationGplas 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\n\nContacta.c.schurch@umcutrecht.nl

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Arredondo-Alonso, S., Bootsma, M., Hein, Y., Rogers, M. R. C., Corander, J., Willems, R. J., Schürch, A. C.. 2019-11-08. gplas: a comprehensive tool for plasmid analysis using short-read graphs. https://doi.org/10.1101/835900

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