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United States Department of Agriculture

Agricultural Research Service

Research Project: ENVIRONMENTALLY SOUND MANURE MANAGEMENT FOR REDUCTION OF GAS EMISSIONS, NUTRIENTS, AND PATHOGENS

Location: Agroecosystem Management Research

Title: Megraft: A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes

Authors
item Bengtsson, Johan -
item Hartmann, Martin -
item Unterseher, Martin -
item Vaishampayan, Parag -
item Abarenkov, Kessy -
item Durso, Lisa
item Bik, Elisabeth -
item Garey, James -
item Eriksson, K. Martin -
item Nilsson, R. Henrik -

Submitted to: Research in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 26, 2012
Publication Date: August 29, 2012
Citation: Bengtsson, J., Hartmann, M., Unterseher, M., Vaishampayan, P.A., Abarenkov, K., Durso, L.M., Bik, E.M., Garey, J.R., Eriksson, K., Nilsson, R. 2012. Megraft: A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes. Research in Microbiology. 163:407-412. DOI: 10.1016J.RESMIC.2012.07.001.

Interpretive Summary: Metagenomics is a recent field of research that allows researchers to identify all of the bacteria and other organisms (and genes) in environmental samples based on specific DNA sequences that serve as nametags for each microbe. In order to figure out if one has looked at enough nametags to accurately describe all of the microbes in a sample, a sequence rarefaction test is run. The rarefaction test, however, was originally designed to be used with other sequencing technologies, and it is difficult to accurately apply this test with the new metagenomic methods. To solve this problem, a new way of running the rarefaction test was developed and a software package – Megraft – that allows researchers to run the rarefaction test using new metagenomic data sets was introduced.

Technical Abstract: Metagenomic libraries represent subsamples of the total DNA found at a study site and offer unprecedented opportunities to study ecological and functional aspects of microbial communities. To examine the depth of the sequencing effort, rarefaction analysis of the ribosomal small sub-unit (SSU/16S/18S) gene in the metagenome is usually performed. The fragmentary nature of SSU sequences in next-generation sequencing libraries poses a problem to this analysis, however. We introduce a software package – Megraft – that grafts SSU fragments onto full-length SSU sequences, accounting for observed and unobserved variability, for accurate assessment of species richness and sequencing depth in metagenomics endeavors.

Last Modified: 11/27/2014