Parallel sorting by regular sampling
Journal of Parallel and Distributed Computing
Introduction to parallel computing: design and analysis of algorithms
Introduction to parallel computing: design and analysis of algorithms
Communication operations on coarse-grained mesh architectures
Parallel Computing
C3: a parallel model for coarse-grained machines
Journal of Parallel and Distributed Computing
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Bioinformatics
Bioinformatics
Bioinformatics
ZOOM! Zillions of oligos mapped
Bioinformatics
Bioinformatics
Bioinformatics
Multiple Sequence Alignment System for Pyrosequencing Reads
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
Bioinformatics
Journal of Parallel and Distributed Computing
Bioinformatics
Proceedings of the 2013 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining
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Genome resequencing with short reads generated from pyrosequencing generally relies on mapping the short reads against a single reference genome. However, mapping of reads from multiple reference genomes is not possible using a pairwise mapping algorithm. In order to align the reads w.r.t each other and the reference genomes, existing multiple sequence alignment(MSA) methods cannot be used because they do not take into account the position of these short reads with respect to the genome, and are highly inefficient for a large number of sequences. In this paper, we develop a highly scalable parallel algorithm based on domain decomposition, referred to as P-Pyro-Align, to align such a large number of reads from single or multiple reference genomes. The proposed alignment algorithm accurately aligns the erroneous reads, and has been implemented on a cluster of workstations using MPI library. Experimental results for different problem sizes are analyzed in terms of execution time, quality of the alignments, and the ability of the algorithm to handle reads from multiple haplotypes. We report high quality multiple alignment of up to 0.5 million reads. The algorithm is shown to be highly scalable and exhibits super-linear speedups with increasing number of processors.