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Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

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      QIIME allows analysis of high-throughput community sequencing data.

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        Search and clustering orders of magnitude faster than BLAST.

         Robert Edgar (2010)
        Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets. Binaries are available at no charge for non-commercial use at http://www.drive5.com/usearch.
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          Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.

          mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.
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            Author and article information

            Journal
            Molecular Ecology
            Mol Ecol
            Wiley-Blackwell
            09621083
            November 2017
            November 26 2017
            : 26
            : 21
            : 5872-5895
            10.1111/mec.14350
            © 2017

            http://doi.wiley.com/10.1002/tdm_license_1.1

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