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NRGC: a novel referential genome compression algorithm

Author:
Saha, Subrata, Rajasekaran, Sanguthevar
Source:
Bioinformatics 2016 v.32 no.22 pp. 3405-3412
ISSN:
1460-2059
Subject:
Internet, algorithms, bioinformatics, genome, high-throughput nucleotide sequencing, humans, nucleotide sequences
Abstract:
Motivation: Next-generation sequencing techniques produce millions to billions of short reads. The procedure is not only very cost effective but also can be done in laboratory environment. The state-of-the-art sequence assemblers then construct the whole genomic sequence from these reads. Current cutting edge computing technology makes it possible to build genomic sequences from the billions of reads within a minimal cost and time. As a consequence, we see an explosion of biological sequences in recent times. In turn, the cost of storing the sequences in physical memory or transmitting them over the internet is becoming a major bottleneck for research and future medical applications. Data compression techniques are one of the most important remedies in this context. We are in need of suitable data compression algorithms that can exploit the inherent structure of biological sequences. Although standard data compression algorithms are prevalent, they are not suitable to compress biological sequencing data effectively. In this article, we propose a novel referential genome compression algorithm (NRGC) to effectively and efficiently compress the genomic sequences. Results: We have done rigorous experiments to evaluate NRGC by taking a set of real human genomes. The simulation results show that our algorithm is indeed an effective genome compression algorithm that performs better than the best-known algorithms in most of the cases. Compression and decompression times are also very impressive. Availability and Implementation: The implementations are freely available for non-commercial purposes. They can be downloaded from: http://www.engr.uconn.edu/~rajasek/NRGC.zip Contact: rajasek@engr.uconn.edu
Agid:
6247587