Acceleration of short and long DNA read mapping without loss of accuracy using suffix array

Bioinformatics

Volumn 30, Issue 23, 2014, Pages 3396-3398

  Tárraga, Joaquín ^a   Arnau, Vicente ^b   Martínez, Héctor ^c   Moreno, Raul ^d   Cazorla, Diego ^d   Salavert Torres, José ^e   Blanquer Espert, Ignacio ^e,f   Dopazo, Joaquín ^a,g   Medina, Ignacio ^a,h  

^a CENTRO DE INVESTIGACIÓN PRÍNCIPE FELIPE   (Spain)

^b UNIVERSITY OF VALENCIA   (Spain)

^c UNIVERSITAT JAUME I   (Spain)

^d INSTITUTO DE INVESTIGACIÓN EN INFORMÁTICA DE ALBACETE   (Spain)

^e INSTITUTO DE INSTRUMENTACIÓN PARA IMAGEN MOLECULAR I3M   (Spain)

^f HOSPITAL UNIVERSITARIO LA FE   (Spain)

^g CENTRO DE INVESTIGACIÓN BIOMÉDICA EN RED DE ENFERMEDADES RARAS CIBERER   (Spain)

^h WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANIMAL; COMPUTER PROGRAM; DNA SEQUENCE; DROSOPHILA; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; PROCEDURES; SEQUENCE ALIGNMENT;

ALGORITHMS; ANIMALS; DROSOPHILA; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84925553260     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu553     Document Type: Article

References (15)

1. Biesecker, L.G. (2010) Exome sequencing makes medical genomics a reality. Nat. Genet., 42, 13-14.
2. Bussotti, G. et al. (2011) BlastR-fast and accurate database searches for noncoding RNAs. Nucleic Acids Res., 39, 6886-6895.
3. Chaisson, M.J. and Tesler, G. (2012) Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics, 13, 238.
4. Chen, Y. et al. (2013) CGAP-align: a high performance DNA short read alignment tool. PLoS One, 8, e61033.
5. Dobin, A. et al. (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29, 15-21.
6. Fonseca, N.A. et al. (2012) Tools for mapping high-throughput sequencing data. Bioinformatics, 28, 3169-3177.
7. Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
8. Li, H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv, 1303.3997.
9. Liu, C.M. et al. (2012) SOAP3: ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics, 28, 878-879.
10. Mamber, U. and Myers, G. (1993) Suffix arrays: a new method for on-line string searches. SIAM J. Comput., 22, 935-948.
11. McKenna, A. et al. (2010) The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res., 20, 1297-1303.
12. Raczy, C. et al. (2013) Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms. Bioinformatics, 29, 2041-2043.
13. Rognes, T. and Seeberg, E. (2000) Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors. Bioinformatics, 16, 699-706.
14. Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
15. Watson, M. (2014) Illuminating the future of DNA sequencing. Genome Biol., 15, 108.