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CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment.

Jeongsu Oh1, Chi-Hwan Choi2, Min-Kyu Park3

  • 1Microbial Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.

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|March 9, 2016
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Summary
This summary is machine-generated.

CLUSTOM-CLOUD is a novel distributed sequence clustering program that efficiently processes large 16S rRNA datasets using In-Memory Data Grid technology. It offers enhanced scalability and accuracy for microbial diversity analysis in bioinformatics.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Microbial Ecology

Background:

  • High-throughput sequencing generates vast amounts of 16S rRNA reads for microbial diversity analysis.
  • Clustering these reads into operational taxonomic units (OTUs) is crucial for downstream bioinformatics tasks.
  • Existing clustering algorithms struggle with the scale of modern sequencing data.

Purpose of the Study:

  • To develop a scalable and accurate distributed sequence clustering program for large 16S rRNA datasets.
  • To leverage In-Memory Data Grid (IMDG) technology for enhanced computational performance.

Main Methods:

  • CLUSTOM-CLOUD, a distributed sequence clustering program utilizing IMDG technology.
  • Evaluation on 16S rRNA human microbiome datasets in laboratory and cloud environments.
  • Comparative accuracy testing against existing tools using mock community pyrosequences.

Main Results:

  • CLUSTOM-CLOUD efficiently processed large datasets, e.g., 200K reads in ~3 hours on 10 nodes.
  • Scalability demonstrated in cloud environments, processing 1 million reads in 11-20 hours with 20-40 nodes.
  • Achieved higher accuracy than DOTUR, mothur, ESPRIT-Tree, UCLUST, and Swarm in comparative tests.

Conclusions:

  • CLUSTOM-CLOUD effectively handles large-scale 16S rRNA sequence data, outperforming its predecessor CLUSTOM.
  • The program offers significant computational scalability and high accuracy for microbial diversity analysis.
  • CLUSTOM-CLOUD represents a significant advancement for bioinformatics analysis of microbial communities.