BAMBAM: PARALLEL COMPARATIVE ANALYSIS OF HIGH-THROUGHPUT SEQUENCING DATA
First Claim
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1. An generic analysis system comprising:
- a data storage device storing a first aligned read file and a second aligned read file, where each file comprises genetic aligned sequence reads that include genomic location information; and
an analysis engine coupled with the data storage device and configured to;
obtain a first aligned sequence read from the first aligned read file and a second aligned sequence read from the second aligned read file;
align the first aligned sequence read and the second aligned sequence read through their respective genomic location information to form a local alignment between the first and second aligned sequence reads;
generate a local differential sequence between the first and the second aligned sequence reads within the local alignment;
update a differential genetic sequence object according to the local differential sequence; and
cause the differential genetic sequence object to be stored on a second storage device.
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Abstract
A differential sequence object is constructed on the basis of alignment of sub-strings via incremental synchronization of sequence strings using known positions of the sub-strings relative to a reference genome sequence. An output file is then generated that comprises only relevant changes with respect to the reference genome.
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18 Claims
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1. An generic analysis system comprising:
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a data storage device storing a first aligned read file and a second aligned read file, where each file comprises genetic aligned sequence reads that include genomic location information; and an analysis engine coupled with the data storage device and configured to; obtain a first aligned sequence read from the first aligned read file and a second aligned sequence read from the second aligned read file;
align the first aligned sequence read and the second aligned sequence read through their respective genomic location information to form a local alignment between the first and second aligned sequence reads;generate a local differential sequence between the first and the second aligned sequence reads within the local alignment; update a differential genetic sequence object according to the local differential sequence; and cause the differential genetic sequence object to be stored on a second storage device. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18)
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Specification