  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.
  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 naive exhaustive approach.
  Availability: Squeezambler and datasets are available under
http://compbio.cs.wayne.edu/software/squeezambler/.
