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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, vol. 16, 2015, doi:10.1186/s12859-015-0533-0.
APA
Vyverman, M., De Baets, B., Fack, V., & Dawyndt, P. (2015). A long fragment aligner called ALFALFA. BMC BIOINFORMATICS, 16. https://doi.org/10.1186/s12859-015-0533-0
Chicago author-date
Vyverman, Michaël, Bernard De Baets, Veerle Fack, and Peter Dawyndt. 2015. “A Long Fragment Aligner Called ALFALFA.” BMC BIOINFORMATICS 16. https://doi.org/10.1186/s12859-015-0533-0.
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. doi:10.1186/s12859-015-0533-0.
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://doi.org/10.1186/s12859-015-0533-0}},
  volume       = {{16}},
  year         = {{2015}},
}

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