Hash-based efficient comparison of sequencing results
AssigneeSharecare AI, Inc.
InventorsGeert Trooskens, Wim Maria R. Van Criekinge
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Abstract
The technology disclosed generates a reference array of variant data for locations that are shared between read results which are to be compared, and generates hashes over a selected pattern length of positions in the reference array to independently produce non-unique window hashes for base patterns in the read results. It then selects for comparison window hashes that occur less than a ceiling number of times and compares the selected window hashes to identify common window hashes between the read results. It then determines a similarity measure for the read results based on the common window hashes.
Claims27
A computer-implemented method of efficiently comparing read results, the method including:
- generating a reference array of variant data for locations shared between read results to be compared;
- generating hashes over a selected pattern length of positions in the reference array to independently produce non-unique window hashes for base patterns in the read results;
- selecting for comparison window hashes that occur less than a ceiling number of times;
- comparing the selected window hashes to identify common window hashes between the read results;
- and
- determining a similarity measure for the read results based on the common window hashes.
A system including one or more processors coupled to memory, the memory loaded with computer instructions to efficiently compare read results, the instructions, when executed on the processors, implement actions comprising:
- generating a reference array of variant data for locations shared between read results to be compared;
- generating hashes over a selected pattern length of positions in the reference array to independently produce non-unique window hashes for base patterns in the read results;
- selecting for comparison window hashes that occur less than a ceiling number of times;
- comparing the selected window hashes to identify common window hashes between the read results;
- and
- determining a similarity measure for the read results based on the common window hashes.
A computer-implemented method of efficiently comparing sequenced files, the method including:
- accessing a first sequenced file and a second sequenced file, wherein the first and second sequenced files contain variants occurring at different carriers and at different carrier positions;
- generating a reference array for those carrier positions that are shared between the first and second sequenced files;
- based on the reference array, generating a first sequence from the first sequenced file and a second sequence from the second sequenced file;
- generating hashes over a selected pattern length of positions in the reference array to independently produce non-unique window hashes for base patterns in the first and second sequences;
- selecting for comparison window hashes that occur less than a ceiling number of times;
- comparing the selected window hashes to identify common window hashes between the first and second sequences;
- and
- determining a similarity measure between the first and second sequences based on the common window hashes.
Dependencies are inferred from the claim text.