Methods and systems for storing sequence read data

• US 9,292,527 B2
• Filed: 01/23/2015
• Issued: 03/22/2016
• 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 J
• Application Number:
  US14/604,165
• Publication Number:
  US 20150149510A1
• Time in Patent Office: 424 Days
• Field of Search: 341/87, 702/19, 702/20, 435/91.52, 435/6.12, 435/6, 435/6.1
• US Class Current: 1/1
• 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:

sequencing a nucleic acid from a sample to generate a plurality of sequence reads;

identifying one or more sets of duplicative sequence reads within the plurality of sequence reads;

storing only one sequence read from each of the one or more sets of duplicative sequence in a master read file;

collecting meta information for each of the plurality of sequence reads, appending the meta information into a compressed file, and matching the meta information to a single read in the master read file; and

later retrieving the plurality of sequence reads from the compressed file and the master read file.

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

obtaining a plurality of sequence reads from a sample by sequencing a nucleic acid from the sample;

identifying one or more sets of duplicative sequence reads within the plurality of sequence reads;

storing in a master read file only one sequence read from each of the one or more sets of duplicative sequence reads; and

separately retrieving the plurality of sequence reads from the master read file.

3. A method for using stored sequence read data, the method comprising:

using a computer system comprising a memory coupled to a processor for;

obtaining 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, retrieving an associated read from the master sequence read file and appending 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.

4. The method of claim 3, wherein the master sequence read file, the compressed file, and the output sequence read file each have a format that is human-readable.

5. The method of claim 4, wherein sequence reads are stored in the master sequence read file and the output sequence read file using IUPAC characters.

6. The method of claim 4, wherein the format of the output sequence read file is one selected from the group consisting of:

a FASTA file;

a FASTQ file; and

a VCF file.

7. The method of claim 4, wherein the format of the master sequence read file is a text file.

8. The method of claim 4, wherein the computer system comprises a text editor program capable of opening the files having the format.

9. The method of claim 8, wherein the text editor program is capable of displaying the files on a computer screen showing the metadata and the sequence reads in a human-readable format.

10. The method of claim 3, wherein each line of metadata comprises a sequence read ID.

11. The method of claim 3, wherein the output sequence read file contains a perfectly lossless retrieval of the sequence reads obtained from the sample.

12. The method of claim 3, further comprising obtaining the master sequence read file and the compressed file by:

sequencing a nucleic acid from the sample to generate the sequence reads;

identifying the one or more sets of duplicative sequence reads within the sequence reads; and

storing the only one sequence read from each of the one or more sets of duplicative sequence reads in the master read file.