DySC: software for greedy clustering of 16S rRNA reads

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 a...

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Bibliographic Details
Published in:Bioinformatics 2012-08, Vol.28 (16), p.2182-2183
Main Authors: ZEJUN ZHENG, KRAMER, Stefan, SCHMIDT, Bertil
Format: Article
Language:English
Subjects:
Bioinformatics
Biological and medical sciences
Cadmium
Cluster Analysis
Clustering
Computer programs
Dynamics
Fundamental and applied biological sciences. Psychology
General aspects
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Metagenome
Microorganisms
RNA, Ribosomal, 16S - genetics
Run time (computers)
Sequence Analysis, RNA - methods
Software
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Summary: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. DySC, implemented in C, is available at http://code.google.com/p/dysc/ under GNU GPL license.
ISSN:1367-4803
1367-4811
1460-2059
DOI:10.1093/bioinformatics/bts355