This thesis presents a new approach towards de novo DNA assembly for short reads. Its two main contributions are a novel, robust filtering scheme for noisy reads that outperforms the (accuracy of the) widely used Sasson’s filter, and a novel assembly algorithm that, minimizing space and maximizing locality of accesses, runs faster than all state-of-the-art algorithms even when on substantially cheaper hardware

Towards locality aware de novo dna assembly of short reads in colour space

Cappelleri, Vincenzo Maria
2011/2012

Abstract

This thesis presents a new approach towards de novo DNA assembly for short reads. Its two main contributions are a novel, robust filtering scheme for noisy reads that outperforms the (accuracy of the) widely used Sasson’s filter, and a novel assembly algorithm that, minimizing space and maximizing locality of accesses, runs faster than all state-of-the-art algorithms even when on substantially cheaper hardware
2011-12-13
76
DNA, SOLiD, colour, filter, Sasson, assembly, de novo, Velvet, Abyss, locality, hash, memory
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/20.500.12608/15386