METAREP：JCVI 宏基因组学报告——一个用于高性能比较宏基因组学的开源工具。
METAREP: JCVI metagenomics reports--an open source tool for high-performance comparative metagenomics.
机构信息
The J. Craig Venter Institute, Rockville, MD 20850, USA.
出版信息
Bioinformatics. 2010 Oct 15;26(20):2631-2. doi: 10.1093/bioinformatics/btq455. Epub 2010 Aug 26.
SUMMARY
JCVI Metagenomics Reports (METAREP) is a Web 2.0 application designed to help scientists analyze and compare annotated metagenomics datasets. It utilizes Solr/Lucene, a high-performance scalable search engine, to quickly query large data collections. Furthermore, users can use its SQL-like query syntax to filter and refine datasets. METAREP provides graphical summaries for top taxonomic and functional classifications as well as a GO, NCBI Taxonomy and KEGG Pathway Browser. Users can compare absolute and relative counts of multiple datasets at various functional and taxonomic levels. Advanced comparative features comprise statistical tests as well as multidimensional scaling, heatmap and hierarchical clustering plots. Summaries can be exported as tab-delimited files, publication quality plots in PDF format. A data management layer allows collaborative data analysis and result sharing.
AVAILABILITY
Web site http://www.jcvi.org/metarep; source code http://github.com/jcvi/METAREP CONTACT: syooseph@jcvi.org
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
JCVI 宏基因组学报告（METAREP）是一个 Web 2.0 应用程序，旨在帮助科学家分析和比较已注释的宏基因组数据集。它利用 Solr/Lucene，一个高性能可扩展的搜索引擎，快速查询大型数据集。此外，用户可以使用类似 SQL 的查询语法来筛选和精炼数据集。METAREP 提供了顶级分类学和功能分类的图形摘要，以及 GO、NCBI 分类学和 KEGG 途径浏览器。用户可以在各种功能和分类学水平上比较多个数据集的绝对和相对计数。高级比较功能包括统计检验以及多维缩放、热图和层次聚类图。摘要可以以制表符分隔的文件导出，也可以以 PDF 格式的出版质量图导出。数据管理层允许协作数据分析和结果共享。
网址
http://www.jcvi.org/metarep；源代码：http://github.com/jcvi/METAREP
联系人
补充信息
补充数据可在 Bioinformatics 在线获得。
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