Sequence assembly and consensus sequence determination
AssigneePacific Biosciences of California, Inc.
InventorsAaron Klammer, Susan Tang, Mark Chaisson, Jon Sorenson, Chen-Shan Chin
Life of this patent
Estimating the term…
Abstract
Computer implemented methods, and systems performing such methods for processing signal data from analytical operations and systems, and particularly in processing signal data from sequence-by-incorporation processes to identify nucleotide sequences of template nucleic acids and larger nucleic acid molecules, e.g., genomes or fragments thereof. In particularly preferred embodiments, nucleic acid sequences generated by such methods are subjected to de novo assembly and/or consensus sequence determination.
Claims25
1-38. (canceled)
A method identifying regions of sequence overlap between sequencing contigs, the method comprising:
- a) deriving a plurality of first sequencing contigs from a first plurality of sequencing reads from a first sequencing method;
- b) deriving a second plurality of second sequencing contigs from a second plurality of sequencing reads from a second sequencing method, wherein the first and second sequencing methods are different from one another;
- c) incorporating the first sequencing contigs-and the second sequencing contigs into a data structure;
- d) generating a set of k-mers;
- e) searching the data structure for regions of the sequencing contigs that match a first k-mers of the set of k-mers, wherein the regions are identified as regions of sequence overlap between the first sequencing contigs and the second sequencing contigs;
- and
- f) repeating step e with further k-mers in the set of k-mers to identify further regions of sequence overlap between the first sequencing contigs and the second sequencing contigs.
(canceled)
A method of aligning a sequence read to a reference sequence, comprising:
- a) finding matches of short subsequences of the sequence read in the reference sequence;
- b) identifying regions within the reference sequence having a plurality of matches to the subsequences of the sequence read;
- c) scoring the plurality of matches;
- and
- d) aligning the plurality of matches.
(canceled)
A system for generating a consensus sequence, comprising:
- a) computer memory containing a set of sequence reads;
- b) computer-readable code for applying an overlap detection algorithm to the set of sequence reads and generating a set of detected overlaps between pairs of the sequence reads;
- c) computer-readable code for assembling the set of sequence reads into an ordered layout based upon the set of detected overlaps;
- and
- d) memory for storing the ordered layout generated in step c.
57-59. (canceled)
Dependencies are inferred from the claim text.