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Updated: Feb 12, 2026

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
Published on: March 15, 2019
PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads
Märt Roosaare1, Mikk Puustusmaa1, Märt Möls1,2
1Department of Bioinformatics, IMCB, University of Tartu, Tartu, Estonia.
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.
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