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

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...

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Autores principales: Arredondo-Alonso, Sergio, Bootsma, Martin, Hein, Yaïr, Rogers, Malbert R C, Corander, Jukka, Willems, Rob J L, Schürch, Anita C
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7320608/
https://www.ncbi.nlm.nih.gov/pubmed/32271863
http://dx.doi.org/10.1093/bioinformatics/btaa233
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author Arredondo-Alonso, Sergio
Bootsma, Martin
Hein, Yaïr
Rogers, Malbert R C
Corander, Jukka
Willems, Rob J L
Schürch, Anita C
author_facet Arredondo-Alonso, Sergio
Bootsma, Martin
Hein, Yaïr
Rogers, Malbert R C
Corander, Jukka
Willems, Rob J L
Schürch, Anita C
author_sort Arredondo-Alonso, Sergio
collection PubMed
description 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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spelling pubmed-73206082020-07-01 gplas: a comprehensive tool for plasmid analysis using short-read graphs Arredondo-Alonso, Sergio Bootsma, Martin Hein, Yaïr Rogers, Malbert R C Corander, Jukka Willems, Rob J L Schürch, Anita C Bioinformatics Applications Notes 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. Oxford University Press 2020-04-09 2020-06-15 /pmc/articles/PMC7320608/ /pubmed/32271863 http://dx.doi.org/10.1093/bioinformatics/btaa233 Text en © The Author(s) 2020. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Arredondo-Alonso, Sergio
Bootsma, Martin
Hein, Yaïr
Rogers, Malbert R C
Corander, Jukka
Willems, Rob J L
Schürch, Anita C
gplas: a comprehensive tool for plasmid analysis using short-read graphs
title gplas: a comprehensive tool for plasmid analysis using short-read graphs
title_full gplas: a comprehensive tool for plasmid analysis using short-read graphs
title_fullStr gplas: a comprehensive tool for plasmid analysis using short-read graphs
title_full_unstemmed gplas: a comprehensive tool for plasmid analysis using short-read graphs
title_short gplas: a comprehensive tool for plasmid analysis using short-read graphs
title_sort gplas: a comprehensive tool for plasmid analysis using short-read graphs
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7320608/
https://www.ncbi.nlm.nih.gov/pubmed/32271863
http://dx.doi.org/10.1093/bioinformatics/btaa233
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