DySC：用于 16S rRNA reads 贪心聚类的软件。

DySC: software for greedy clustering of 16S rRNA reads.

机构信息

Institut für Informatik, Johannes Gutenberg University Mainz, Mainz 55099, Germany.

出版信息

Bioinformatics. 2012 Aug 15;28(16):2182-3. doi: 10.1093/bioinformatics/bts355. Epub 2012 Jun 23.

DOI:10.1093/bioinformatics/bts355

PMID:22730435

Abstract

UNLABELLED

Pyrosequencing technologies are frequently used for sequencing the 16S ribosomal RNA marker gene for profiling microbial communities. Clustering of the produced reads is an important but time-consuming task. We present Dynamic Seed-based Clustering (DySC), a new tool based on the greedy clustering approach that uses a dynamic seeding strategy. Evaluations based on the normalized mutual information (NMI) criterion show that DySC produces higher quality clusters than UCLUST and CD-HIT at a comparable runtime.

AVAILABILITY AND IMPLEMENTATION

DySC, implemented in C, is available at http://code.google.com/p/dysc/ under GNU GPL license.

摘要

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焦磷酸测序技术常用于对 16S 核糖体 RNA 标记基因进行微生物群落分析。产生的读取数据聚类是一项重要但耗时的任务。我们提出了基于动态种子的聚类（DySC），这是一种新的工具，基于贪婪聚类方法，并使用动态种子策略。基于归一化互信息（NMI）标准的评估表明，DySC 在可比的运行时间内产生的聚类比 UCLUST 和 CD-HIT 具有更高的质量。