bfast an alignment tool for large scale genome resequencingbfast大规模基因组重测序的校准工具.pdfVIP

BFAST: An Alignment Tool for Large Scale Genome Resequencing 1,2 2 2 Nils Homer , Barry Merriman *, Stanley F. Nelson 1 Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America, 2 Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America Abstract 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