Sparse Tensor Decomposition for Haplotype Assembly of Diploids and Polyploids

Abstract

ABSTRACTA framework that formulates haplotype assembly as sparse tensor decomposition is proposed. The problem is cast as that of decomposing a tensor having special structural constraints and missing a large fraction of its entries into a product of two factors, U and ; tensor reveals haplotype information while U is a sparse matrix encoding the origin of erroneous sequencing reads. An algorithm, AltHap, which reconstructs haplotypes of either diploid or poly-ploid organisms by solving this decomposition problem is proposed. Starting from a judiciously selected initial point, AltHap alternates between two optimization tasks to recover U and by relying on a modified gradient descent search that exploits salient structural properties of U and . The performance and convergence properties of AltHap are theoretically analyzed and, in doing so, guarantees on the achievable minimum error correction scores and correct phasing rate are established. AltHap was tested in a number of different scenarios and was shown to compare favorably to state-of-the-art methods in applications to haplotype assembly of diploids, and significantly outperform existing techniques when applied to haplotype assembly of polyploids.