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BFAST: an alignment tool for large scale genome resequencing.

BACKGROUND: The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence reads to a large reference genome. Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25-100 base range, in the presence of errors and true biological variation. METHODOLOGY: We introduce a new algorithm specifically optimized for this task, as well as a freely available implementation, BFAST, which can align data produced by any of current sequencing platforms, allows for user-customizable levels of speed and accuracy, supports paired end data, and provides for efficient parallel and multi-threaded computation on a computer cluster. The new method is based on creating flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary multiple independent indexes allowed to achieve robustness against read errors and sequence variants. The final local alignment uses a Smith-Waterman method, with gaps to support the detection of small indels. CONCLUSIONS: We compare BFAST to a selection of large-scale alignment tools -- BLAT, MAQ, SHRiMP, and SOAP -- in terms of both speed and accuracy, using simulated and real-world datasets. We show BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods. We show BFAST can align the amount of data needed to fully resequence a human genome, one billion reads, with high sensitivity and accuracy, on a modest computer cluster in less than 24 hours. BFAST is available at (

Pubmed ID: 19907642


  • Homer N
  • Merriman B
  • Nelson SF


PloS one

Publication Data

November 12, 2009

Associated Grants

  • Agency: NIMH NIH HHS, Id: R01 MH071852
  • Agency: NINDS NIH HHS, Id: U24 NS052108

Mesh Terms

  • Algorithms
  • Computational Biology
  • Computer Simulation
  • Genetic Techniques
  • Genetic Variation
  • Genome, Human
  • Humans
  • Reproducibility of Results
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Software