PT  - JOURNAL ARTICLE
AU  - Roye Rozov
AU  - Aya Kav Brown
AU  - David Bogumil
AU  - Eran Halperin
AU  - Itzhak Mizrahi
AU  - Ron Shamir
TI  - Recycler: an algorithm for detecting plasmids from de novo assembly graphs
AID  - 10.1101/029926
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 029926
4099  - http://biorxiv.org/content/early/2015/10/28/029926.short
4100  - http://biorxiv.org/content/early/2015/10/28/029926.full
AB  - Plasmids have garnered a great deal of interest in recent years. They are known to have important roles in antibiotic resistance and in affecting production of metabolites used in industrial and agricultural applications. However, their extraction through deep sequencing remains challenging, in spite of rapid drops in costs for data acquisition and rapid increases in sequencer output. Here, we attempt to ameliorate this situation by introducing a new plasmid-specific assembly algorithm, leveraging assembly graphs and contigs provided by a conventional de novo assembler. We introduce the first plasmid-specific short read assembly tool, called Recycler, and demonstrate its merits in comparison with extant approaches. We show on simulated and real data that Recycler greatly increases the number of true plasmids recovered while remaining highly accurate. On simulated plasmidomes, Recycler showed approximately 40% increase in the proportion of true plasmids recovered over naive assembly in several cases. We validate these results on real data, by comparison against available reference sequences and quantifying annotation of predicted ORFs. Recycler recovered 4 out of 5 known plasmids in assembly of an E. Coli strain, and generated plasmids in high agreement with known plasmid annotation on real plasmidome data. Moreover, 6 out of 8 plasmids previously validated by PCR were completely recovered. Recycler is available at http://github.com/rozovr/Recycler