US 12,597,491 B2Granted

Method and apparatus for compressing fastq data through character frequency-based sequence reordering

AssigneePusan National University Industry-University Cooperation Foundation

InventorsGiltae Song, Dohyeon Lee

Life of this patent

Estimating the term…

Loading patent…

Abstract

A method and apparatus for decompressing FASTQ data through character frequency-based sequence reordering implemented by a computer apparatus, the method including separating genome sequencing data into components of an identifier, a nucleotide sequence read, and prediction quality information; measuring character frequency for the entire data of each of the nucleotide sequence read and the prediction quality information; producing a score by applying the measured character frequency for the nucleotide sequence read and the prediction quality information; reordering the nucleotide sequence read and the prediction quality information based on a condition that is preset based on the score; and compressing at least one of information of the identifier, an identifier of the nucleotide sequence read, and an identifier of the prediction quality information through a compression program by including the reordered nucleotide sequence read and the reordered prediction quality information and generating compressed genome sequencing data.

Claims19

Dependent claims

A method of compressing genome sequencing data in FASTQ format through character frequency-based sequence reordering implemented by a computer apparatus, the method comprising:

providing a computer having a processor and a memory coupled to the processor, wherein the memory contains genome sequencing data in FASTQ format;
using the processor to separate the genome sequencing data into components of an identifier, a nucleotide sequence read, and prediction quality information;
using the processor to measure character frequency for the entire data of each of the nucleotide sequence read and the prediction quality information and omitting any nucleotide having a first percentage frequency below a first threshold and any prediction quality having a second percentage frequency information below a second threshold;
using the processor to produce a score for each nucleotide read that is comprised of a front digit from a rounded distribution of each letter distribution in the genome sequencing data and the letter distribution in the genome sequencing data from the measured character frequency for the nucleotide sequence read and the prediction quality information;
using the processor to reorder the nucleotide sequence read and the prediction quality information based on the score;
and
using the processor to compress at least one of information of the identifier, an identifier of the nucleotide sequence read, and an identifier of the prediction quality information through a compression program by including the reordered nucleotide sequence read and the reordered prediction quality information and generating compressed genome sequencing data.

4 more elements

An apparatus for compressing genome sequencing data in FASTQ format through character frequency-based sequence reordering implemented by a computer apparatus, the apparatus comprising:

a computer having a processor and a memory coupled to the processor, wherein the memory contains genome sequencing data and wherein the processor is programmed to include a genome sequencing data separator configured to separate the genome sequencing data into components of an identifier, a nucleotide sequence read, and prediction quality information;
wherein the processor is further programmed to include a character frequency measurer configured to measure character frequency for the entire data of each of the nucleotide sequence read and the prediction quality information and omitting any nucleotide having a first percentage frequency below a first threshold and any prediction quality having a second percentage frequency information below a second threshold;
wherein the processor is further programmed to include a score producer configured to produce a score for each nucleotide read that is comprised of a front digit from a rounded distribution of each letter distribution in the genome sequencing data and the letter distribution in the genome sequencing data from the measured character frequency for the nucleotide sequence read and the prediction quality information;
wherein the processor is further programmed to include a score-based sorter configured to reorder the nucleotide sequence read and the prediction quality information based on the score;
and
wherein the processor is further programmed to include a genome sequencing data compressor configured to compress at least one of information of the identifier, an identifier of the nucleotide sequence read, and an identifier of the prediction quality information through a compression program by including the reordered nucleotide sequence read and the reordered prediction quality information and to generate compressed genome sequencing data.

3 more elements

Dependencies are inferred from the claim text.

Facts

Application: 17/536,046Filed 28 Nov 2021
Priority: KR 10-2020-017963221 Dec 2020
Published: US 2022/0199202 A123 Jun 2022
Granted: 7 Apr 2026
Term ends: Not estimatedThe source records don’t support an estimate.

Classification4 codes

G16B 50/50
ICT programming tools or database systems specially adapted for bioinformatics: compression of genetic data
G06F 16/1744
Redundancy elimination performed by the file system: using compression, e.g. sparse files
G16B
Bioinformatics, i.e. information and communication technology [ict] specially adapted for genetic or
G06F
Computing and data processing