Living in an Ivory Basement Stochastic thoughts on science, testing, and programming.

Assembling the heck out of soil - paper posted

We just posted yet another pre-submission paper to arXiv.org:

Assembling large, complex environmental metagenomes

Authors: Adina Chuang Howe, Janet Jansson, Stephanie A. Malfatti, Susannah Tringe, James M. Tiedje, and C. Titus Brown

Abstract:

The large volumes of sequencing data required to deeply sample complex environments pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources. We apply two data reduction approaches, digital normalization and partitioning, to this challenge. Using a human gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes from matched Iowa corn and native prairie soils. The predicted functional content and phylogenetic origin of the assembled contigs indicate significant taxonomic differences despite similar function. The assembly strategies presented are generic and can be extended to any metagenome; full source code is freely available under a BSD license.

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This paper combines the approaches described in our partitioning paper (Pell et al, PNAS, 2012), our digital normalization paper, and our Illumina artifacts paper and validates them on the de novo assembly of a human gut "mock" community. We then apply them to two very large soil samples.

--titus

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Living in an Ivory Basement Stochastic thoughts on science, testing, and programming.

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