Monday, May 06, 2013

Squeezambler: Distilled Single Cell Genome Sequencing and De Novo Assembly for Sparse Microbial Communities - implementation -

While decoding the genome is important, it is as important to figure what is where. The following paper provides a means of figuring out all the species in very large microbial samples through  adaptive sensing using the sparsity of the underlying number of species. I am not sure how difficult it is to perform adaptive measurements technologically, but it would be interesting to see if a non adaptive sensing or pooling strategy reaching the k = m + 1 bound would be more interesting technologically speaking. Without further due, here is:   Distilled Single Cell Genome Sequencing and De Novo Assembly for Sparse Microbial Communities by Zeinab Taghavi, Narjes S. Movahedi, Sorin Draghici, Hamidreza Chitsaz

Identification of all species 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 species is usually much smaller than the number of cells. Here, we present a novel divide-and-conquer method to sequence and de novo assemble the genomes of all of the different species present in a microbial sample with a sequencing cost and computational complexity proportional to the number of species, not 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.
Squeezambler and associated datasets are available here.

Probably relevant to this paper is another one from  by Amnon Amir, and Or Zuk featured three years ago, see CS: Bacterial Community Reconstruction Using A Single Sequencing Reaction 

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