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

Sergio Arredondo-Alonso; Martin Bootsma; Yaïr Hein; Malbert R C Rogers; Jukka Corander; Rob J L Willems; Anita C Schürch

doi:10.1093/bioinformatics/btaa233

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

Sergio Arredondo-Alonso, Martin Bootsma, Yaïr Hein, Malbert R C Rogers, Jukka Corander, Rob J L Willems, Anita C Schürch

Research output: Contribution to journal › Article › Academic › peer-review

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.

Original language	English
Pages (from-to)	3874-3876
Number of pages	3
Journal	Bioinformatics
Volume	36
Issue number	12
DOIs	https://doi.org/10.1093/bioinformatics/btaa233
Publication status	Published - 15 Jun 2020

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title = "gplas: a comprehensive tool for plasmid analysis using short-read graphs",

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.",

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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 J L

AU - Schürch, Anita C

PY - 2020/6/15

Y1 - 2020/6/15

N2 - 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.

AB - 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.

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DO - 10.1093/bioinformatics/btaa233

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SN - 1367-4803

VL - 36

SP - 3874

EP - 3876

JO - Bioinformatics

JF - Bioinformatics

IS - 12

ER -

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

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