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

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

SUBMITTER: Roosaare M 

PROVIDER: S-EPMC5885972 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature