RT Journal
A1 Antipov, Dmitry
A1 Raiko, Mikhail
A1 Lapidus, Alla
A1 Pevzner, Pavel A.
T1 Plasmid detection and assembly in genomic and metagenomic data sets
JF Genome Research 
JO Genome Research 
YR 2019 
FD June 01 
VO 29 
IS 6 
SP 961 
OP 968 
DO 10.1101/gr.241299.118 
UL http://genome.cshlp.org/content/29/6/961.abstract 
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.