Abstract

Significance Investigations of complex environments rely on large volumes of sequence data to adequately sample the genetic diversity of a microbial community. The assembly of short-read data into longer, more interpretable sequence currently is not possible for much of the research community because it requires specialized computational facilities. We present approaches that make de novo assembly of complex metagenomes more accessible. These approaches scale data size with community richness and subdivide the data into tractable subsets representing individual species. We applied these methods toward the assembly of two large soil metagenomes to identify important metagenomic references and show that considerably more data are needed to study the terrestrial microbiome comprehensively.

Keywords

MetagenomicsComputational biologyBiologyGenomeSequence assemblyContigGeneGeneticsTranscriptome

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Publication Info

Year
2014
Type
article
Volume
111
Issue
13
Pages
4904-4909
Citations
342
Access
Closed

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Cite This

Adina Chuang Howe, Janet Jansson, Stephanie Malfatti et al. (2014). Tackling soil diversity with the assembly of large, complex metagenomes. Proceedings of the National Academy of Sciences , 111 (13) , 4904-4909. https://doi.org/10.1073/pnas.1402564111

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DOI
10.1073/pnas.1402564111