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

http://www.ncbi.nlm.nih.gov/pubmed/22730435

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.

Pubmed ID: 22730435 RIS Download

Mesh terms: Cluster Analysis | Metagenome | RNA, Ribosomal, 16S | Sequence Analysis, RNA | Software