SG11202102591TA - Fpga-based resequencing analysis method and device - Google Patents

Fpga-based resequencing analysis method and device

Info

Publication number
SG11202102591TA
SG11202102591TA SG11202102591TA SG11202102591TA SG11202102591TA SG 11202102591T A SG11202102591T A SG 11202102591TA SG 11202102591T A SG11202102591T A SG 11202102591TA SG 11202102591T A SG11202102591T A SG 11202102591TA SG 11202102591T A SG11202102591T A SG 11202102591TA
Authority
SG
Singapore
Prior art keywords
fpga
analysis method
based resequencing
resequencing analysis
resequencing
Prior art date
Application number
SG11202102591TA
Inventor
Yinlong Xie
Weihua Huang
Chen Chen
Jingbo Tang
Original Assignee
Mgi Tech Co Ltd
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Mgi Tech Co Ltd filed Critical Mgi Tech Co Ltd
Publication of SG11202102591TA publication Critical patent/SG11202102591TA/en

Links

Classifications

    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10Sequence alignment; Homology search
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06FELECTRIC DIGITAL DATA PROCESSING
    • G06F30/00Computer-aided design [CAD]
    • G06F30/30Circuit design
    • G06F30/32Circuit design at the digital level
    • G06F30/33Design verification, e.g. functional simulation or model checking
    • G06F30/3308Design verification, e.g. functional simulation or model checking using simulation
    • G06F30/331Design verification, e.g. functional simulation or model checking using simulation with hardware acceleration, e.g. by using field programmable gate array [FPGA] or emulation
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06FELECTRIC DIGITAL DATA PROCESSING
    • G06F30/00Computer-aided design [CAD]
    • G06F30/20Design optimisation, verification or simulation
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06FELECTRIC DIGITAL DATA PROCESSING
    • G06F9/00Arrangements for program control, e.g. control units
    • G06F9/06Arrangements for program control, e.g. control units using stored programs, i.e. using an internal store of processing equipment to receive or retain programs
    • G06F9/30Arrangements for executing machine instructions, e.g. instruction decode
    • G06F9/30098Register arrangements
    • G06F9/3012Organisation of register space, e.g. banked or distributed register file
    • G06F9/30123Organisation of register space, e.g. banked or distributed register file according to context, e.g. thread buffers
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06FELECTRIC DIGITAL DATA PROCESSING
    • G06F9/00Arrangements for program control, e.g. control units
    • G06F9/06Arrangements for program control, e.g. control units using stored programs, i.e. using an internal store of processing equipment to receive or retain programs
    • G06F9/30Arrangements for executing machine instructions, e.g. instruction decode
    • G06F9/34Addressing or accessing the instruction operand or the result ; Formation of operand address; Addressing modes
    • G06F9/345Addressing or accessing the instruction operand or the result ; Formation of operand address; Addressing modes of multiple operands or results
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06FELECTRIC DIGITAL DATA PROCESSING
    • G06F9/00Arrangements for program control, e.g. control units
    • G06F9/06Arrangements for program control, e.g. control units using stored programs, i.e. using an internal store of processing equipment to receive or retain programs
    • G06F9/46Multiprogramming arrangements
    • G06F9/48Program initiating; Program switching, e.g. by interrupt
    • G06F9/4806Task transfer initiation or dispatching
    • G06F9/4843Task transfer initiation or dispatching by program, e.g. task dispatcher, supervisor, operating system
    • G06F9/4881Scheduling strategies for dispatcher, e.g. round robin, multi-level priority queues
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00Computing arrangements based on biological models
    • G06N3/12Computing arrangements based on biological models using genetic models
    • G06N3/126Evolutionary algorithms, e.g. genetic algorithms or genetic programming
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Landscapes

  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Theoretical Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Software Systems (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Physics & Mathematics (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Computer Hardware Design (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Computation (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biotechnology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Geometry (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Artificial Intelligence (AREA)
  • Data Mining & Analysis (AREA)
  • Computing Systems (AREA)
  • Computational Linguistics (AREA)
  • Mathematical Physics (AREA)
  • Biomedical Technology (AREA)
  • Physiology (AREA)
  • Bioethics (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Public Health (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
SG11202102591TA 2018-10-23 2018-10-23 Fpga-based resequencing analysis method and device SG11202102591TA (en)

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
PCT/CN2018/111357 WO2020082224A1 (en) 2018-10-23 2018-10-23 Fpga-based resequencing analysis method and device

Publications (1)

Publication Number Publication Date
SG11202102591TA true SG11202102591TA (en) 2021-04-29

Family

ID=70330861

Family Applications (1)

Application Number Title Priority Date Filing Date
SG11202102591TA SG11202102591TA (en) 2018-10-23 2018-10-23 Fpga-based resequencing analysis method and device

Country Status (7)

Country Link
US (1) US11836430B2 (en)
EP (1) EP3852111A4 (en)
JP (1) JP7334244B2 (en)
KR (1) KR20210091126A (en)
CN (1) CN113168888A (en)
SG (1) SG11202102591TA (en)
WO (1) WO2020082224A1 (en)

Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN115691672B (en) * 2022-12-20 2023-06-16 臻和(北京)生物科技有限公司 Base quality value correction method and device for sequencing platform characteristics, electronic equipment and storage medium

Family Cites Families (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2014516514A (en) * 2011-04-14 2014-07-17 コンプリート・ジェノミックス・インコーポレイテッド Processing and analysis of complex nucleic acid sequence data
EP2634717A2 (en) * 2012-02-28 2013-09-04 Koninklijke Philips Electronics N.V. Compact next generation sequencing dataset and efficient sequence processing using same
US9600625B2 (en) 2012-04-23 2017-03-21 Bina Technologies, Inc. Systems and methods for processing nucleic acid sequence data
US9679104B2 (en) 2013-01-17 2017-06-13 Edico Genome, Corp. Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
US9436565B2 (en) * 2013-07-04 2016-09-06 Altera Corporation Non-intrusive monitoring and control of integrated circuits
CN105631239B (en) * 2014-10-30 2018-08-17 国际商业机器公司 Method and apparatus for managing gene order
CN104462211B (en) * 2014-11-04 2018-01-02 北京诺禾致源科技股份有限公司 The processing method and processing unit of weight sequencing data
AU2015349725B2 (en) 2014-11-21 2022-02-03 Research Institute At Nationwide Children's Hospital Parallel-processing systems and methods for highly scalable analysis of biological sequence data
US10192026B2 (en) 2015-03-05 2019-01-29 Seven Bridges Genomics Inc. Systems and methods for genomic pattern analysis
US20170270245A1 (en) * 2016-01-11 2017-09-21 Edico Genome, Corp. Bioinformatics systems, apparatuses, and methods for performing secondary and/or tertiary processing
CN107194204A (en) * 2017-05-22 2017-09-22 人和未来生物科技(长沙)有限公司 A kind of sequencing data of whole genome calculates deciphering method
CN107609350B (en) 2017-09-08 2020-04-03 厦门极元科技有限公司 Data processing method of second-generation sequencing data analysis platform

Also Published As

Publication number Publication date
WO2020082224A1 (en) 2020-04-30
CN113168888A (en) 2021-07-23
EP3852111A1 (en) 2021-07-21
EP3852111A4 (en) 2022-04-20
US20220058321A1 (en) 2022-02-24
JP7334244B2 (en) 2023-08-28
JP2022504611A (en) 2022-01-13
US11836430B2 (en) 2023-12-05
KR20210091126A (en) 2021-07-21

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