title: A Long Fragment Aligner called ALFALFA.
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 .
authors.affiliation: Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 Building S9, Ghent, B-9000, Belgium. Michael.Vyverman@UGent.be.
authors.forename: Michaël
authors.initials: M
authors.lastname: Vyverman
authors.affiliation: Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure links 653, Ghent, B-9000, Belgium. Bernard.DeBaets@UGent.be.
authors.forename: Bernard De
authors.initials: BD
authors.lastname: Baets
authors.affiliation: Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 Building S9, Ghent, B-9000, Belgium. Veerle.Fack@UGent.be.
authors.forename: Veerle
authors.initials: V
authors.lastname: Fack
authors.affiliation: Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 Building S9, Ghent, B-9000, Belgium. Peter.Dawyndt@UGent.be.
authors.forename: Peter
authors.initials: P
authors.lastname: Dawyndt
mesh_terms: D000465:Algorithms; D005075:Biological Evolution; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D057188:Workflow