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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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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cited_by cdi_FETCH-LOGICAL-c452t-ae06a9ef37e9e37f5bc1c101759694066b172db88a27bac22261c7247e2c1473
cites cdi_FETCH-LOGICAL-c452t-ae06a9ef37e9e37f5bc1c101759694066b172db88a27bac22261c7247e2c1473
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container_issue 16
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container_title Bioinformatics
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creator ZEJUN ZHENG
KRAMER, Stefan
SCHMIDT, Bertil
description 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.
doi_str_mv 10.1093/bioinformatics/bts355
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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
title DySC: software for greedy clustering of 16S rRNA reads
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