- Author
- Michaël Vyverman (UGent) , Bernard De Baets (UGent) , Veerle Fack (UGent) and Peter Dawyndt (UGent)
- Organization
- Project
- 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: http://hdl.handle.net/1854/LU-6979318
- 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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