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Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

Published on: April 14, 2016

DySC: software for greedy clustering of 16S rRNA reads

Zejun Zheng¹, Stefan Kramer, Bertil Schmidt

¹Institut für Informatik, Johannes Gutenberg University Mainz, Mainz 55099, Germany.

Bioinformatics (Oxford, England)

|June 26, 2012

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.

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