Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp

Frontiers in Microbiology

Carmen Li¹  Dan Liu²  Manuel Kleiner²  Christine E. Sharp²  Erin Thorson²  Xiaoli Dong²  Marc Strous² 

[1] Department of Biological Sciences, University of CalgaryCalgary, AB, Canada;Department of Geoscience, University of CalgaryCalgary, AB, Canada;

关键词: metagenomics;    amplicon sequencing;    bioinformatics;    microbial ecology;    microbiome;   

DOI  :  10.3389/fmicb.2017.01461

来源: DOAJ

【 摘 要 】

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 2 years ago, MetaAmp has been used >2,800 times, by many users worldwide.

【 授权许可】

Unknown