title: Recycler: an algorithm for detecting plasmids from de novo assembly graphs.
abstract: Plasmids and other mobile elements are central contributors to microbial evolution and genome innovation. Recently, they have been found to have important roles in antibiotic resistance and in affecting production of metabolites used in industrial and agricultural applications. However, their characterization through deep sequencing remains challenging, in spite of rapid drops in cost and throughput increases for sequencing. Here, we attempt to ameliorate this situation by introducing a new circular element assembly algorithm, leveraging assembly graphs provided by a conventional de novo assembler and alignments of paired-end reads to assemble cyclic sequences likely to be plasmids, phages and other circular elements.
  
  
  
  We introduce Recycler, the first tool that can extract complete circular contigs from sequence data of isolate microbial genomes, plasmidome and metagenome sequence data. We show that Recycler greatly increases the number of true plasmids recovered relative to other approaches while remaining highly accurate. We demonstrate this trend via simulations of plasmidomes, comparisons of predictions with reference data for isolate samples, and assessments of annotation accuracy on metagenome data. In addition, we provide validation by DNA amplification of 77 plasmids predicted by Recycler from the different sequenced samples in which Recycler showed mean accuracy of 89% across all data types-isolate, microbiome and plasmidome.
  
  
  
  Recycler is available at http://github.com/Shamir-Lab/Recycler.
  
  
  
  imizrahi@bgu.ac.il.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv, Israel.
authors.forename: Roye
authors.initials: R
authors.lastname: Rozov
authors.affiliation: The Department of Life Sciences & the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
authors.forename: Aya
authors.initials: A
authors.lastname: Brown Kav
authors.affiliation: The Department of Life Sciences & the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
authors.forename: David
authors.initials: D
authors.lastname: Bogumil
authors.affiliation: The Department of Life Sciences & the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
authors.forename: Naama
authors.initials: N
authors.lastname: Shterzer
authors.affiliation: Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv, Israel.|Molecular Microbiology and Biotechnology Department, Tel-Aviv University, Tel Aviv, Israel.|International Computer Science Institute, Berkeley, CA, USA.
authors.forename: Eran
authors.initials: E
authors.lastname: Halperin
authors.affiliation: The Department of Life Sciences & the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
authors.forename: Itzhak
authors.initials: I
authors.lastname: Mizrahi
authors.affiliation: Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv, Israel.
authors.forename: Ron
authors.initials: R
authors.lastname: Shamir
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D054892:Metagenome; D010957:Plasmids; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software