TY - JOUR

T1 - Plasmid detection and assembly in genomic and metagenomic datasets

AU - Antipov, D.

AU - Raiko, M.

AU - Lapidus, A.

AU - Pevzner, P.A.

PY - 2019/1/1

Y1 - 2019/1/1

N2 - Although plasmids are important for bacterial survival and adaptation, plasmid detection and assembly from genomic, let alone metagenomic, samples remain challenging. The recently developed plasmidSPAdes assembler addressed some of these challenges in the case of isolate genomes but stopped short of detecting plasmids in metagenomic assemblies, an untapped source of yet to be discovered plasmids. We present the metaplasmidSPAdes tool for plasmid assembly in metagenomic data sets that reduced the false positive rate of plasmid detection compared with the state-of-the-art approaches. We assembled plasmids in diverse data sets and have shown that thousands of plasmids remained below the radar in already completed genomic and metagenomic studies. Our analysis revealed the extreme variability of plasmids and has led to the discovery of many novel plasmids (including many plasmids carrying antibiotic-resistance genes) without significant similarities to currently known ones.

AB - Although plasmids are important for bacterial survival and adaptation, plasmid detection and assembly from genomic, let alone metagenomic, samples remain challenging. The recently developed plasmidSPAdes assembler addressed some of these challenges in the case of isolate genomes but stopped short of detecting plasmids in metagenomic assemblies, an untapped source of yet to be discovered plasmids. We present the metaplasmidSPAdes tool for plasmid assembly in metagenomic data sets that reduced the false positive rate of plasmid detection compared with the state-of-the-art approaches. We assembled plasmids in diverse data sets and have shown that thousands of plasmids remained below the radar in already completed genomic and metagenomic studies. Our analysis revealed the extreme variability of plasmids and has led to the discovery of many novel plasmids (including many plasmids carrying antibiotic-resistance genes) without significant similarities to currently known ones.

UR - http://www.scopus.com/inward/record.url?scp=85067903478&partnerID=8YFLogxK

UR - http://www.mendeley.com/research/plasmid-detection-assembly-genomic-metagenomic-data-sets

U2 - 10.1101/gr.241299.118

DO - 10.1101/gr.241299.118

M3 - Article

C2 - 31048319

VL - 29

SP - 961

EP - 968

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 6

ER -