Methods and systems for storing sequence read data
First Claim
Patent Images
1. A system for storing sequence read data, the system comprising:
- a processor coupled to a non-transitory memory containing instructions executable by the processor to cause the system to;
obtain a plurality of sequence reads from a sample;
identify one or more sets of duplicative sequence reads within the plurality of sequence reads;
store only one sequence read from each of the one or more sets of duplicative sequence in a master read file;
collect meta information for each of the plurality of sequence reads, append the meta information into a compressed file, and match the meta information to a single read in the master read file; and
later retrieve the plurality of sequence reads from the compressed file and the master read file.
8 Assignments
0 Petitions
Accused Products
Abstract
The present invention generally relates to storing sequence read data. The invention can involve obtaining a plurality of sequence reads from a sample, identifying one or more sets of duplicative sequence reads within the plurality of sequence reads, and storing only one of the sequence reads from each set of duplicative sequence reads in a text file using nucleotide characters.
-
Citations
11 Claims
-
1. A system for storing sequence read data, the system comprising:
a processor coupled to a non-transitory memory containing instructions executable by the processor to cause the system to; obtain a plurality of sequence reads from a sample; identify one or more sets of duplicative sequence reads within the plurality of sequence reads; store only one sequence read from each of the one or more sets of duplicative sequence in a master read file; collect meta information for each of the plurality of sequence reads, append the meta information into a compressed file, and match the meta information to a single read in the master read file; and later retrieve the plurality of sequence reads from the compressed file and the master read file.
-
2. A system for storing sequence read data, the system comprising:
a processor coupled to a non-transitory memory containing instructions executable by the processor to cause the system to; obtain a plurality of sequence reads from a sample; identify one or more sets of duplicative sequence reads within the plurality of sequence reads; store in a master read file only one sequence read from each of the one or more sets of duplicative sequence reads; and separately retrieve the plurality of sequence reads from the master read file.
-
3. A system for using stored sequence read data, the system comprising:
-
a processor coupled to a non-transitory memory containing instructions executable by the processor to cause the system to; obtain a master sequence read file that includes only one sequence read from each of one or more sets of duplicative sequence reads obtained from a sample and a compressed file that includes lines of metadata for the sequence reads obtained from the sample; for each line of metadata in the compressed file, retrieve an associated read from the master sequence read file and append that line of metadata and the associated read to an output sequence read file, wherein the output sequence read file contains the sequence reads as originally obtained from the sample. - View Dependent Claims (4, 5, 6, 7, 8, 9, 10, 11)
-
Specification