PT  - JOURNAL ARTICLE
AU  - Arredondo-Alonso, Sergio
AU  - Bootsma, Martin
AU  - Hein, Yaïr
AU  - Rogers, Malbert R.C.
AU  - Corander, Jukka
AU  - Willems, Rob JL
AU  - Schürch, Anita C.
TI  - gplas: a comprehensive tool for plasmid analysis using short-read graphs
AID  - 10.1101/835900
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 835900
4099  - http://biorxiv.org/content/early/2019/11/08/835900.short
4100  - http://biorxiv.org/content/early/2019/11/08/835900.full
AB  - Summary Plasmids 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.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.gitContact a.c.schurch{at}umcutrecht.nl