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A long fragment aligner called ALFALFA

Michaël Vyverman (UGent) , Bernard De Baets (UGent) , Veerle Fack (UGent) and Peter Dawyndt (UGent)
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Abstract
Background: Rapid evolutions in sequencing technology force read mappers into flexible adaptation to longer reads, changing error models, memory barriers and novel applications. Results: ALFALFA achieves a high performance in accurately mapping long single-end and paired-end reads to gigabase-scale reference genomes, while remaining competitive for mapping shorter reads. Its seed-and-extend workflow is underpinned by fast retrieval of super-maximal exact matches from an enhanced sparse suffix array, with flexible parameter tuning to balance performance, memory footprint and accuracy. Conclusions: ALFALFA is open source and available at http://alfalfa.ugent.be.
Keywords
READ ALIGNMENT, VERSATILE, ACCURATE, GENOME, BURROWS-WHEELER TRANSFORM, Paired-end reads, Enhanced sparse suffix array, Long read mapping, Super-maximal exact matches

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Please use this url to cite or link to this publication:

MLA
Vyverman, Michaël et al. “A Long Fragment Aligner Called ALFALFA.” BMC BIOINFORMATICS 16 (2015): n. pag. Print.
APA
Vyverman, M., De Baets, B., Fack, V., & Dawyndt, P. (2015). A long fragment aligner called ALFALFA. BMC BIOINFORMATICS, 16.
Chicago author-date
Vyverman, Michaël, Bernard De Baets, Veerle Fack, and Peter Dawyndt. 2015. “A Long Fragment Aligner Called ALFALFA.” Bmc Bioinformatics 16.
Chicago author-date (all authors)
Vyverman, Michaël, Bernard De Baets, Veerle Fack, and Peter Dawyndt. 2015. “A Long Fragment Aligner Called ALFALFA.” Bmc Bioinformatics 16.
Vancouver
1.
Vyverman M, De Baets B, Fack V, Dawyndt P. A long fragment aligner called ALFALFA. BMC BIOINFORMATICS. 2015;16.
IEEE
[1]
M. Vyverman, B. De Baets, V. Fack, and P. Dawyndt, “A long fragment aligner called ALFALFA,” BMC BIOINFORMATICS, vol. 16, 2015.
@article{6979318,
  abstract     = {Background: Rapid evolutions in sequencing technology force read mappers into flexible adaptation to longer reads, changing error models, memory barriers and novel applications. 
Results: ALFALFA achieves a high performance in accurately mapping long single-end and paired-end reads to gigabase-scale reference genomes, while remaining competitive for mapping shorter reads. Its seed-and-extend workflow is underpinned by fast retrieval of super-maximal exact matches from an enhanced sparse suffix array, with flexible parameter tuning to balance performance, memory footprint and accuracy. 
Conclusions: ALFALFA is open source and available at http://alfalfa.ugent.be.},
  articleno    = {159},
  author       = {Vyverman, Michaël and De Baets, Bernard and Fack, Veerle and Dawyndt, Peter},
  issn         = {1471-2105},
  journal      = {BMC BIOINFORMATICS},
  keywords     = {READ ALIGNMENT,VERSATILE,ACCURATE,GENOME,BURROWS-WHEELER TRANSFORM,Paired-end reads,Enhanced sparse suffix array,Long read mapping,Super-maximal exact matches},
  language     = {eng},
  pages        = {11},
  title        = {A long fragment aligner called ALFALFA},
  url          = {http://dx.doi.org/10.1186/s12859-015-0533-0},
  volume       = {16},
  year         = {2015},
}

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