Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes.

ABSTRACT: Shotgun metagenomic sequencing does not depend on gene-targeted primers or PCR amplification; thus, it is not affected by primer bias or chimeras. However, searching rRNA genes from large shotgun Illumina data sets is computationally expensive, and no approach exists for unsupervised community analysis of small-subunit (SSU) rRNA gene fragments retrieved from shotgun data. We present a pipeline, SSUsearch, to achieve the faster identification of short-subunit rRNA gene fragments and enabled unsupervised community analysis with shotgun data. It also includes classification and copy number correction, and the output can be used by traditional amplicon analysis platforms. Shotgun metagenome data using this pipeline yielded higher diversity estimates than amplicon data but retained the groupin

SUBMITTER: Guo J 

PROVIDER: S-EPMC4702641 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature