Dataset Information

HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences.

ABSTRACT:

Motivation

Nucleotide sequence data are being produced at an ever increasing rate. Clustering such sequences by similarity is often an essential first step in their analysis-intended to reduce redundancy, define gene families or suggest taxonomic units. Exact clustering algorithms, such as hierarchical clustering, scale relatively poorly in terms of run time and memory usage, yet they are desirable because heuristic shortcuts taken during clustering might have unintended consequences in later analysis steps.

Results

Here we present HPC-CLUST, a highly optimized software pipeline that can cluster large numbers of pre-aligned DNA sequences by running on distributed computing hardware. It allocates both memory and computing resources efficiently, and can process more than a million sequences in a few hours on a small cluster.

Availability and implementation

Source code and binaries are freely available at http://meringlab.org/software/hpc-clust/; the pipeline is implemented in Cþþ and uses the Message Passing Interface (MPI) standard for distributed computing.

SUBMITTER: Matias Rodrigues JF

PROVIDER: S-EPMC3892691 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

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Publications

HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences.

Matias Rodrigues João F JF von Mering Christian C

Bioinformatics (Oxford, England) 20131109 2

<h4>Motivation</h4>Nucleotide sequence data are being produced at an ever increasing rate. Clustering such sequences by similarity is often an essential first step in their analysis-intended to reduce redundancy, define gene families or suggest taxonomic units. Exact clustering algorithms, such as hierarchical clustering, scale relatively poorly in terms of run time and memory usage, yet they are desirable because heuristic shortcuts taken during clustering might have unintended consequences in ...[more]

PMID: 24215029

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Dataset Information

HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences.

Motivation

Results

Availability and implementation

Publications

HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences.

Similar Datasets

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