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HIVE-hexagon: high-performance, parallelized sequence alignment for next-generation sequencing data analysis.

ABSTRACT:

Unlabelled

Due to the size of Next-Generation Sequencing data, the computational challenge of sequence alignment has been vast. Inexact alignments can take up to 90% of total CPU time in bioinformatics pipelines. High-performance Integrated Virtual Environment (HIVE), a cloud-based environment optimized for storage and analysis of extra-large data, presents an algorithmic solution: the HIVE-hexagon DNA sequence aligner. HIVE-hexagon implements novel approaches to exploit both characteristics of sequence space and CPU, RAM and Input/Output (I/O) architecture to quickly compute accurate alignments. Key components of HIVE-hexagon include non-redundification and sorting of sequences; floating diagonals of linearized dynamic programming matrices; and consideration of cross-similarity to minimize computations.

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https://hive.biochemistry.gwu.edu/hive/

SUBMITTER: Santana-Quintero L

PROVIDER: S-EPMC4053384 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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HIVE-hexagon: high-performance, parallelized sequence alignment for next-generation sequencing data analysis.

Santana-Quintero Luis L Dingerdissen Hayley H Thierry-Mieg Jean J Mazumder Raja R Simonyan Vahan V

PloS one 20140611 6

<h4>Unlabelled</h4>Due to the size of Next-Generation Sequencing data, the computational challenge of sequence alignment has been vast. Inexact alignments can take up to 90% of total CPU time in bioinformatics pipelines. High-performance Integrated Virtual Environment (HIVE), a cloud-based environment optimized for storage and analysis of extra-large data, presents an algorithmic solution: the HIVE-hexagon DNA sequence aligner. HIVE-hexagon implements novel approaches to exploit both characteris ...[more]

PMID: 24918764

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