HIVE-hexagon: high-performance, parallelized sequence alignment for next-generation sequencing data analysis.
basic_science · Level V
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- Record sourced from PubMed, PMID 24918764.
- Also identified by DOI 10.1371/journal.pone.0099033 and PMC identifier 4053384.
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Abstract
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. https://hive.biochemistry.gwu.edu/hive/
Medical subject headings
- Sequence Alignment
- Sequence Analysis, DNA