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
Artikel i vetenskaplig tidskrift, 2012

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.

Species richness analysis

Metagenomics

diversitetsanalys

rDNA

18S

16S

Rarefaction

Författare

Johan Bengtsson

Göteborgs universitet

Martin Hartmann

Martin Unterseher

Parag Vaishampayan

Kessy Abarenkov

Lisa Durso

Elisabeth M. Bik

James R. Garey

Martin Eriksson

Göteborgs universitet

R. Henrik Nilsson

Göteborgs universitet

Research in Microbiology

0923-2508 (ISSN)

Vol. 163 407-412

Ämneskategorier

Biologisk systematik

Mikrobiologi

Bioinformatik och systembiologi

DOI

10.1016/j.resmic.2012.07.001

PubMed

22824070