Methods and systems for storing sequence read data

• US 8,847,799 B1
• Filed: 06/02/2014
• Issued: 09/30/2014
• Est. Priority Date: 06/03/2013
• Status: Active Grant

• Current Assignee: Invitae Corporation
• Original Assignee: Good Start Genetics, Inc. (Invitae Corporation)
• Inventors: Kennedy, Caleb J., Chennagiri, Niru
• Primary Examiner(s): Lauture, Joseph
• Application Number:
  US14/293,568
• Time in Patent Office: 120 Days
• Field of Search: 341/87, 702/19, 702/20, 435/91.52, 435/6.12, 435/6, 435/6.1
• US Class Current: 341/87
• CPC Class Codes: C12N 15/10 Processes for the isolation, preparation or purification of DNA or RNA chemical preparation of DNA or RNA C07H21/00; preparation of non-structural polynucleotides from microorganisms or with enzymes C12P19/34
• CPC Class Codes: C12Q 1/44 involving esterase
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: G06F 16/164 File meta data generation
• CPC Class Codes: G06F 16/1744 using compression, e.g. sparse files
• CPC Class Codes: G06N 3/123 DNA computing
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 30/20 Sequence assembly
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/50 Compression of genetic data
• CPC Class Codes: G16B 99/00 Subject matter not provided for in other groups of this subclass
• CPC Class Codes: G16H 10/40 for data related to laboratory analysis, e.g. patient specimen analysis
• CPC Class Codes: G16H 50/00 ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
• CPC Class Codes: H03M 7/30 Compression speech analysis-synthesis for redundancy reduction G10L19/00; for image communication H04N; Expansion; Suppression of unnecessary data, e.g. redundancy reduction
• CPC Class Codes: H03M 7/3059 Digital compression and data reduction techniques where the original information is represented by a subset or similar information, e.g. lossy compression
• CPC Class Codes: H03M 7/70 Type of the data to be coded, other than image and sound
• CPC Class Codes: H04L 67/10 : in which an application is distributed across nodes in the network software deployment G06F8/60; multiprogramming arrangements G06F9/46

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.

Claims

1. A method for storing sequence read data, the method comprising:

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 sequence read from each of the one or more sets of duplicative sequence reads.

2. The method according to claim 1, wherein obtaining the plurality of sequence reads comprises sequencing a nucleic acid from the sample to generate the plurality of sequence reads.

3. The method according to claim 2, wherein sequencing comprises one selected from the group consisting of single molecule sequencing and sequencing by synthesis.

4. The method according claim 1, wherein the sample comprises a human tissue or bodily fluid sample.

5. The method according claim 1, wherein obtaining the plurality of sequence reads comprises obtaining a computer-readable input file.

6. The method according to claim 5, wherein the computer-readable input file is once selected from the group consisting of:

a FASTA file;

a FASTQ file; and

a VCF file.

7. The method according to claim 1, further comprising storing the only one sequence read from each of the one or more sets of duplicative sequence reads in at least one master sequence read file.

8. The method according to claim 7, wherein the at least one master sequence read file is a text file.

9. The method according to claim 7, further comprising collecting meta information for each of the plurality of sequence reads and matching the meta information to a single read in the at least one master sequence read file.

10. The method according to claim 9, wherein the meta information comprises a sequence read ID.

11. The method according to claim 9, wherein the obtaining, identifying, and storing steps are performed by a computer system comprising a processor coupled to a non-transitory memory, and further wherein the collected and matched meta information is stored in a computer-readable output file.

12. The method of claim 11, wherein the sequence reads are stored in the at least one master sequence read file using IUPAC nucleotide characters.

13. The method of claim 12, wherein the at least one master sequence read file and the output file are stored as plain text files, and further wherein the computer system comprises a text editor program capable of opening the plain text files.

14. The method of claim 13, wherein the text editor program is capable of displaying the plain text files on a computer screen showing the meta information and the sequence reads in a human-readable format.

15. The method of claim 7, wherein sequence reads are stored in the at least one master sequence read file using IUPAC nucleotide characters.