title: Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities.
abstract: BACKGROUND
  Identification of every single genome present in a microbial sample is an important and challenging task with crucial applications. It is challenging because there are typically millions of cells in a microbial sample, the vast majority of which elude cultivation. The most accurate method to date is exhaustive single-cell sequencing using multiple displacement amplification, which is simply intractable for a large number of cells. However, there is hope for breaking this barrier, as the number of different cell types with distinct genome sequences is usually much smaller than the number of cells.
  
  
  RESULTS
  Here, we present a novel divide and conquer method to sequence and de novo assemble all distinct genomes present in a microbial sample with a sequencing cost and computational complexity proportional to the number of genome types, rather than the number of cells. The method is implemented in a tool called Squeezambler. We evaluated Squeezambler on simulated data. The proposed divide and conquer method successfully reduces the cost of sequencing in comparison with the naïve exhaustive approach.
  
  
  BACKGROUND
  Squeezambler and datasets are available at http://compbio.cs.wayne.edu/software/squeezambler/.
authors.affiliation: Department of Computer Science and Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48202, USA.
authors.forename: Zeinab
authors.initials: Z
authors.lastname: Taghavi
authors.forename: Narjes S
authors.initials: NS
authors.lastname: Movahedi
authors.forename: Sorin
authors.initials: S
authors.lastname: Draghici
authors.forename: Hamidreza
authors.initials: H
authors.lastname: Chitsaz
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D064349:Genome, Microbial; D006801:Humans; D007422:Intestines / Q000382:microbiology; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid
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