Pileup File Generation from Compressed Genomic Data

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Solution Overview

Problem

Current methods for generating pileup files from compressed next-generation sequencing (NGS) data require complete decompression and reconstruction, leading to high memory usage and processing power consumption, which increases analysis time.

Innovation Solution

A method and device for generating a pileup file by partially decompressing read data from a reference-based compression file to obtain differential strings, which are then decoded using conversion rules to create the pileup file, reducing the need for complete decompression and reconstruction.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Reliability

If complete decompression and reconstruction of compressed genomic data is performed, then accurate pileup file generation is achieved, but memory usage and processing power consumption increase significantly

Engineering Contradiction:

Improveaccuracy of pileup file generationVSAvoidprocessing power consumption

Core Design Contradiction:

ReliabilityVSUse of energy by moving object

Solution Approach 1:

The patent extracts and processes only the essential components needed for pileup file generation from the compressed genomic data, rather than fully decompressing all data. This selective extraction approach maintains accuracy while reducing processing power consumption and memory usage.

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The patent applies partial decompression to generate the pileup file directly from compressed data without complete reconstruction. This partial action approach achieves the necessary accuracy for variation calling while significantly reducing the computational resources required compared to full decompression.

Inventive Principle:

Principle #16Partial or excessive action

2Loss of information

If complete decompression and reconstruction of compressed genomic data is performed, then complete read data is obtained, but analysis time increases

Engineering Contradiction:

Improvecompleteness of genomic dataVSAvoidgenomic data analysis time

Core Design Contradiction:

Loss of informationVSLoss of time

Solution Approach 1:

The patent performs preliminary processing on the compressed data structure to enable direct pileup file generation. By preparing the compressed data in advance with appropriate indexing and structure, the system can extract necessary information without time-consuming full decompression, thus reducing analysis time while maintaining data completeness.

Inventive Principle:

Principle #10Preliminary action

3Adaptability or versatility

If compressed genomic data is fully decompressed, then all read information is accessible, but memory space consumption increases

Engineering Contradiction:

Improveaccessibility of read informationVSAvoidmemory space consumption

Core Design Contradiction:

Adaptability or versatilityVSQuantity of substance

Solution Approach 1:

The patent implements a nested structure where the pileup file generation process operates within the compressed data framework. The system nests the necessary processing logic inside the compressed data structure, allowing direct access to required information without full decompression, thereby reducing memory space consumption while maintaining accessibility.

Inventive Principle:

Principle #7Nested doll (Nesting)

Data Source

PatentUS10394763B2Method and device for generating pileup file from compressed genomic data

Publication Date: 2019.08.27 SAMSUNG ELECTRONICS CO LTD

AI summary

Provided are a method and apparatus for generating a pileup file from a reference-based compression file. The method includes receiving a reference-based compression file comprising a plurality of pieces of read data that are compressed, partially decompressing the plurality of pieces of read data to acquire a differential string associated with the plurality of pieces of read data, and generating the pileup file by decoding the differential string based on a plurality of conversion rules.