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Nucleic acid sequence assembly

  • US 10,318,706 B2
  • Filed: 06/26/2017
  • Issued: 06/11/2019
  • Est. Priority Date: 02/17/2015
  • Status: Active Grant
First Claim
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1. A method for determining locally optimal contig configuration of a plurality of contigs within a cluster, the method comprising:

  • (I) obtaining read pair data mapping to the plurality of contigs within the cluster, wherein read pair data is obtained from a set of paired end reads obtained by digesting sample DNA to generate internal double strand breaks within the DNA, allowing the double strand breaks to re-ligate randomly to form a plurality of re-ligation junctions, and sequencing at each side of the plurality of re-ligation junctions;

    (II) obtaining a set of clustered contigs; and

    (III) processing said set of clustered contigs by;

    (a) identifying a window of size w contigs starting at position i along the set of clustered contigs;

    (b) considering w! 2w ordering and orienting options for contigs of the window of size w contigs by examining scores of orders and orientations of the contigs of the window in each position i in the window;

    (c) orienting and ordering w contigs of the window to obtain an optimal score;

    (d) shifting the window to position i+1 along the set of clustered contigs;

    (e) repeating steps (a), (b) and (c) for said window at position i+1 using the orienting and ordering of w for said window at position i+1 contigs to determine an optimal score, thereby orienting and ordering said plurality of contigs in a locally optimal configuration relative to the score; and

    (f) outputting said locally optimal configuration to a network, screen or server.

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