TY  - JOUR
A1  - Antipov, Dmitry
A1  - Raiko, Mikhail
A1  - Lapidus, Alla
A1  - Pevzner, Pavel A.
T1  - Plasmid detection and assembly in genomic and metagenomic data sets
Y1  - 2019/06/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 961 
EP  - 968 
DO  - 10.1101/gr.241299.118 
VL  - 29 
IS  - 6 
UR  - http://genome.cshlp.org/content/29/6/961.abstract 
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. 
ER  -