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 and similar environmental datasets.

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

Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 11, 405 30 Göteborg, Sweden. johan@microbiology.se

Research in microbiology 2012 Jul

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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 a community sequencing effort, rarefaction analysis of the ribosomal small subunit (SSU/16S/18S) gene in the metagenome is usually performed. The fragmentary, non-overlapping nature of SSU sequences in metagenomic libraries poses a problem for 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. Copyright © 2012 Institut Pasteur. All rights reserved.

Citation

Johan Bengtsson, Martin Hartmann, Martin Unterseher, Parag Vaishampayan, Kessy Abarenkov, Lisa Durso, Elisabeth M Bik, James R Garey, K Martin Eriksson, R Henrik Nilsson. 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 and similar environmental datasets. Research in microbiology. 2012 Jul;163(6-7):407-12