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 .

SUBMITTER: Vyverman M 

PROVIDER: S-EPMC4449525 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature