TY - UNPB
T1 - gplas: a comprehensive tool for plasmid analysis using short-read graphs
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.
PY - 2019
Y1 - 2019
N2 - 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 Contact a.c.schurch{at}umcutrecht.nl
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 Contact a.c.schurch{at}umcutrecht.nl
U2 - 10.1101/835900
DO - 10.1101/835900
M3 - Preprint
BT - gplas: a comprehensive tool for plasmid analysis using short-read graphs
PB - bioRxiv
ER -