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

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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.

Original languageEnglish
Pages (from-to)3874-3876
Number of pages3
JournalBioinformatics (Oxford, England)
Issue number12
Publication statusPublished - 15 Jun 2020


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