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

Authors

Luis Santana-Quintero, US Food and Drug Administration, Rockville, MD
Hayley Dingerdissen, George Washington UniversityFollow
Jean Thierry-Mieg, National Institutes of Health
Raja Mazumder, George Washington University
Vahan Simonyan, US Food and Drug Administration, Rockville, MDFollow

Document Type

Journal Article

Publication Date

6-11-2014

Journal

PLoS ONE

Volume

Volume 9, Issue 6

Inclusive Pages

Article number e99033

DOI

10.1371/journal.pone.0099033

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.

Comments

Reproduced with permission of PLoS ONE.

Creative Commons License

The person who associated a work with this deed has dedicated the work to the public domain by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.

APA Citation

Santana-Quintero, L., Dingerdissen, H., Thierry-Mieg, J., Mazumder, R., Simonyan, V. (2014). HIVE-Hexagon: High-Performance, Parallelized Sequence Alignment for Next-Generation Sequencing Data Analysis. PLoS ONE 9(6): e99033.

Peer Reviewed

1

Open Access

1