PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads

Märt Roosaare; Mikk Puustusmaa; Märt Möls; Mihkel Vaher; Maido Remm

doi:10.7717/peerj.4588

PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads

PeerJ. 2018 Apr 2:6:e4588. doi: 10.7717/peerj.4588. eCollection 2018.

Authors

Märt Roosaare¹, Mikk Puustusmaa¹, Märt Möls^{1

2}, Mihkel Vaher¹, Maido Remm¹

Affiliations

¹ Department of Bioinformatics, IMCB, University of Tartu, Tartu, Estonia.
² Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia.

Abstract

Background: Plasmids play an important role in the dissemination of antibiotic resistance, making their detection an important task. Using whole genome sequencing (WGS), it is possible to capture both bacterial and plasmid sequence data, but short read lengths make plasmid detection a complex problem.

Results: We developed a tool named PlasmidSeeker that enables the detection of plasmids from bacterial WGS data without read assembly. The PlasmidSeeker algorithm is based on k-mers and uses k-mer abundance to distinguish between plasmid and bacterial sequences. We tested the performance of PlasmidSeeker on a set of simulated and real bacterial WGS samples, resulting in 100% sensitivity and 99.98% specificity.

Conclusion: PlasmidSeeker enables quick detection of known plasmids and complements existing tools that assemble plasmids de novo. The PlasmidSeeker source code is stored on GitHub: https://github.com/bioinfo-ut/PlasmidSeeker.

Keywords: Plasmid; Unassembled; Whole genome sequencing; k-mer.

Associated data

figshare/10.6084/m9.figshare.5497972.v1

Grants and funding

This work was supported by the European Union through the European Regional Development Fund through Estonian Centre of Excellence in Genomics and Translational Medicine (project No. 2014-2020.4.01.15-0012) and by the Estonian Ministry of Education and Research (institutional grant IUT34-11). There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.