Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp

被引：68

作者：

Dong, Xiaoli ^{[1
]}

Kleiner, Manuel ^{[1
]}

Sharp, Christine E. ^{[1
]}

Thorson, Erin ^{[1
]}

Li, Carmen ^{[2
]}

Liu, Dan ^{[1
]}

Strous, Marc ^{[1
]}

机构：

[1] Univ Calgary, Dept Geosci, Calgary, AB, Canada

[2] Univ Calgary, Dept Biol Sci, Calgary, AB, Canada

来源：

FRONTIERS IN MICROBIOLOGY | 2017年 / 8卷

基金：

加拿大自然科学与工程研究理事会;

关键词：

metagenomics; amplicon sequencing; bioinformatics; microbial ecology; microbiome; MICROBIAL COMMUNITY STRUCTURE; DIVERSITY; PATTERNS;

D O I：

10.3389/fmicb.2017.01461

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

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.

引用

页数：8

共 28 条

[1] The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature [J].