RT Journal Article
SR Electronic
T1 Fast and simple analysis of MiSeq amplicon sequencing data with MetaAmp
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 131631
DO 10.1101/131631
A1 Xiaoli Dong
A1 Manuel Kleiner
A1 Christine E. Sharp
A1 Erin Thorson
A1 Carmen Li
A1 Dan Liu
A1 Marc Strous
YR 2017
UL http://biorxiv.org/content/early/2017/04/27/131631.abstract
AB Microbial community profiling by barcoded 16S rRNA gene amplicon sequencing currently has many applications in microbial ecology. The low costs of the parallel sequencing of multiplexed samples, combined with the relative ease of data processing and interpretation (compared to shotgun metagenomes) have made this an entry-level approach. Here we present the MetaAmp pipeline for processing of SSU rRNA gene and other non-coding or protein-coding amplicon sequencing data by investigators that are inexperienced with bioinformatics procedures. It accepts single-end or paired-end sequences in fasta or fastq format from various sequencing platforms. It includes read quality control, and merging of forward and reverse reads of paired-end reads. It makes use of UPARSE, Mothur, and the SILVA database for clustering, removal of chimeric reads, taxonomic classification and generation of diversity metrics. The pipeline has been validated with a mock community of known composition. MetaAmp provides a convenient web interface as well as command line interface. It is freely available at: http://ebg.ucalgary.ca/metaamp. Since its launch two years ago, MetaAmp has been used >2,800 times, by many users worldwide.