A Survey of Software and Hardware Approaches to Performing Read Alignment in Next Generation Sequencing.
IEEE/ACM Trans Comput Biol Bioinform
; 14(6): 1202-1213, 2017.
Article
em En
| MEDLINE
| ID: mdl-27362989
ABSTRACT
Computational genomics is an emerging field that is enabling us to reveal the origins of life and the genetic basis of diseases such as cancer. Next Generation Sequencing (NGS) technologies have unleashed a wealth of genomic information by producing immense amounts of raw data. Before any functional analysis can be applied to this data, read alignment is applied to find the genomic coordinates of the produced sequences. Alignment algorithms have evolved rapidly with the advancement in sequencing technology, striving to achieve biological accuracy at the expense of increasing space and time complexities. Hardware approaches have been proposed to accelerate the computational bottlenecks created by the alignment process. Although several hardware approaches have achieved remarkable speedups, most have overlooked important biological features, which have hampered their widespread adoption by the genomics community. In this paper, we provide a brief biological introduction to genomics and NGS. We discuss the most popular next generation read alignment tools and algorithms. Furthermore, we provide a comprehensive survey of the hardware implementations used to accelerate these algorithms.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Alinhamento de Sequência
/
Genômica
/
Sequenciamento de Nucleotídeos em Larga Escala
Limite:
Humans
Idioma:
En
Revista:
ACM Trans Comput Biol Bioinform
Assunto da revista:
BIOLOGIA
/
INFORMATICA MEDICA
Ano de publicação:
2017
Tipo de documento:
Article