title: Bambus 2: scaffolding metagenomes.
abstract: BACKGROUND
  Sequencing projects increasingly target samples from non-clonal sources. In particular, metagenomics has enabled scientists to begin to characterize the structure of microbial communities. The software tools developed for assembling and analyzing sequencing data for clonal organisms are, however, unable to adequately process data derived from non-clonal sources.
  
  
  RESULTS
  We present a new scaffolder, Bambus 2, to address some of the challenges encountered when analyzing metagenomes. Our approach relies on a combination of a novel method for detecting genomic repeats and algorithms that analyze assembly graphs to identify biologically meaningful genomic variants. We compare our software to current assemblers using simulated and real data. We demonstrate that the repeat detection algorithms have higher sensitivity than current approaches without sacrificing specificity. In metagenomic datasets, the scaffolder avoids false joins between distantly related organisms while obtaining long-range contiguity. Bambus 2 represents a first step toward automated metagenomic assembly.
  
  
  BACKGROUND
  Bambus 2 is open source and available from http://amos.sf.net.
  
  
  BACKGROUND
  mpop@umiacs.umd.edu.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Computer Science, University of Maryland, College Park, MD 20742, USA.
authors.forename: Sergey
authors.initials: S
authors.lastname: Koren
authors.forename: Todd J
authors.initials: TJ
authors.lastname: Treangen
authors.forename: Mihai
authors.initials: M
authors.lastname: Pop
mesh_terms: D000465:Algorithms; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D017422:Sequence Analysis, DNA; D012984:Software