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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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Bioinformatics: from nucleotids to networks (N2N)
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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Citation

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

Chicago
Vyverman, Michaël, Bernard De Baets, Veerle Fack, and Peter Dawyndt. 2015. “A Long Fragment Aligner Called ALFALFA.” Bmc Bioinformatics 16.
APA
Vyverman, M., De Baets, B., Fack, V., & Dawyndt, P. (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.
MLA
Vyverman, Michaël, Bernard De Baets, Veerle Fack, et al. “A Long Fragment Aligner Called ALFALFA.” BMC BIOINFORMATICS 16 (2015): n. pag. Print.
@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, Micha{\"e}l and De Baets, Bernard and Fack, Veerle and Dawyndt, Peter},
  issn         = {1471-2105},
  journal      = {BMC BIOINFORMATICS},
  keyword      = {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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