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Accurate long read mapping using enhanced suffix arrays

Michaël Vyverman UGent, Joachim De Schrijver UGent, Wim Van Criekinge UGent, Peter Dawyndt UGent and Veerle Fack UGent (2011) BIOINFORMATICS. p.102-107
abstract
With the rise of high throughput sequencing, new programs have been developed for dealing with the alignment of a huge amount of short read data to reference genomes. Recent developments in sequencing technology allow longer reads, but the mappers for short reads are not suited for reads of several hundreds of base pairs. We propose an algorithm for mapping longer reads, which is based on chaining maximal exact matches and uses heuristics and the Needleman-Wunsch algorithm to bridge the gaps. To compute maximal exact matches we use a specialized index structure, called enhanced suffix array. The proposed algorithm is very accurate and can handle large reads with mutations and long insertions and deletions.
Please use this url to cite or link to this publication:
author
organization
year
type
conference
publication status
published
subject
keyword
SEQUENCE, ALIGNMENT PROGRAM, BURROWS-WHEELER TRANSFORM, Inexact string matching, DNA sequencing, Read mapping, Enhanced suffix arrays
in
BIOINFORMATICS
editor
M Pellegrini, A Fred, J Filipe and H Gamboa
pages
102 - 107
publisher
SciTePress
place of publication
Lisbon, Portugal
conference name
International conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2011)
conference location
Rome, Italy
conference start
2010-01-26
conference end
2010-01-26
Web of Science type
Proceedings Paper
Web of Science id
000308455800018
ISBN
9789898425362
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
P1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1249782
handle
http://hdl.handle.net/1854/LU-1249782
date created
2011-05-31 16:40:14
date last changed
2013-02-27 09:11:32
@inproceedings{1249782,
  abstract     = {With the rise of high throughput sequencing, new programs have been developed for dealing with the alignment of a huge amount of short read data to reference genomes. Recent developments in sequencing technology allow longer reads, but the mappers for short reads are not suited for reads of several hundreds of base pairs. We propose an algorithm for mapping longer reads, which is based on chaining maximal exact matches and uses heuristics and the Needleman-Wunsch algorithm to bridge the gaps. To compute maximal exact matches we use a specialized index structure, called enhanced suffix array. The proposed algorithm is very accurate and can handle large reads with mutations and long insertions and deletions.},
  author       = {Vyverman, Micha{\"e}l and De Schrijver, Joachim and Van Criekinge, Wim and Dawyndt, Peter and Fack, Veerle},
  booktitle    = {BIOINFORMATICS},
  editor       = {Pellegrini, M and Fred, A and Filipe, J and Gamboa, H},
  isbn         = {9789898425362},
  keyword      = {SEQUENCE,ALIGNMENT PROGRAM,BURROWS-WHEELER TRANSFORM,Inexact string matching,DNA sequencing,Read mapping,Enhanced suffix arrays},
  language     = {eng},
  location     = {Rome, Italy},
  pages        = {102--107},
  publisher    = {SciTePress},
  title        = {Accurate long read mapping using enhanced suffix arrays},
  year         = {2011},
}

Chicago
Vyverman, Michaël, Joachim De Schrijver, Wim Van Criekinge, Peter Dawyndt, and Veerle Fack. 2011. “Accurate Long Read Mapping Using Enhanced Suffix Arrays.” In Bioinformatics, ed. M Pellegrini, A Fred, J Filipe, and H Gamboa, 102–107. Lisbon, Portugal: SciTePress.
APA
Vyverman, M., De Schrijver, J., Van Criekinge, W., Dawyndt, P., & Fack, V. (2011). Accurate long read mapping using enhanced suffix arrays. In M. Pellegrini, A. Fred, J. Filipe, & H. Gamboa (Eds.), BIOINFORMATICS (pp. 102–107). Presented at the International conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2011), Lisbon, Portugal: SciTePress.
Vancouver
1.
Vyverman M, De Schrijver J, Van Criekinge W, Dawyndt P, Fack V. Accurate long read mapping using enhanced suffix arrays. In: Pellegrini M, Fred A, Filipe J, Gamboa H, editors. BIOINFORMATICS. Lisbon, Portugal: SciTePress; 2011. p. 102–7.
MLA
Vyverman, Michaël, Joachim De Schrijver, Wim Van Criekinge, et al. “Accurate Long Read Mapping Using Enhanced Suffix Arrays.” Bioinformatics. Ed. M Pellegrini et al. Lisbon, Portugal: SciTePress, 2011. 102–107. Print.