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http://dx.doi.org/10.4014/jmb.1409.09057

Bioinformatic Suggestions on MiSeq-Based Microbial Community Analysis  

Unno, Tatsuya (Faculty of Biotechnology, College of Applied Life Sciences, Jeju National University)
Publication Information
Journal of Microbiology and Biotechnology / v.25, no.6, 2015 , pp. 765-770 More about this Journal
Abstract
Recent sequencing technology development has revolutionized fields of microbial ecology. MiSeq-based microbial community analysis allows us to sequence more than a few hundred samples at a time, which is far more cost-effective than pyrosequencing. The approach, however, has not been preferably used owing to computational difficulties of processing huge amounts of data as well as known Illumina-derived artefact problems with amplicon sequencing. The choice of assembly software to take advantage of paired-end sequencing and methods to remove Illumina artefacts sequences are discussed. The protocol we suggest not only removed erroneous reads, but also dramatically reduced computational workload, which allows even a typical desktop computer to process a huge amount of sequence data generated with Illumina sequencers. We also developed a Web interface (http://biotech.jejunu.ac.kr/ ~abl/16s/) that allows users to conduct fastq-merging and mothur batch creation. The study presented here should provide technical advantages and supports in applying MiSeq-based microbial community analysis.
Keywords
16S rRNA; bioinformatics; microbial community; mothur; pear;
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