Abstract
BackgroundPlasmids 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.ResultsWe 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.ConclusionPlasmidSeeker 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.
Highlights
Plasmids are circular or linear double-stranded DNA molecules capable of autonomous replication and conjugation
Selecting an optimal k-mer length First, we analyzed the effect of k-mer length on the uniqueness of chromosomal k-mers (k-mers that occur only once in the full chromosomal sequence) and on the fraction of k-mers shared between plasmids and chromosomes
Plasmid k-mers that are shared with chromosomal k-mers can hinder plasmid detection
Summary
Plasmids are circular or linear double-stranded DNA molecules capable of autonomous replication and conjugation. They have been described in all three domains of life (Antipov et al, 2016). Pulsed field gel electrophoresis reveals the size and number of plasmids in an isolate, but the process can take several days (Nyberg et al, 2016). Results: We developed a tool named PlasmidSeeker that enables the detection of plasmids from bacterial WGS data without read assembly. The PlasmidSeeker source code is stored on GitHub: https://github.com/bioinfo-ut/PlasmidSeeker
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