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 and similar environmental datasets.
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 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.
authors: Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 11, 405 30 Göteborg, Sweden. johan@microbiology.se
authors: Johan
authors: J
authors: Bengtsson
authors: Martin
authors: M
authors: Hartmann
authors: Martin
authors: M
authors: Unterseher
authors: Parag
authors: P
authors: Vaishampayan
authors: Kessy
authors: K
authors: Abarenkov
authors: Lisa
authors: L
authors: Durso
authors: Elisabeth M
authors: EM
authors: Bik
authors: James R
authors: JR
authors: Garey
authors: K Martin
authors: KM
authors: Eriksson
authors: R Henrik
authors: RH
authors: Nilsson
mesh_terms: D019295:Computational Biology / Q000379:methods*; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics*; D004783:Environmental Microbiology; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D012984:Software
chemical_list: D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012337:RNA, Ribosomal, 18S