CA3174208A1 - Quality score compression - Google Patents

Quality score compression Download PDF

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Publication number
CA3174208A1
CA3174208A1 CA3174208A CA3174208A CA3174208A1 CA 3174208 A1 CA3174208 A1 CA 3174208A1 CA 3174208 A CA3174208 A CA 3174208A CA 3174208 A CA3174208 A CA 3174208A CA 3174208 A1 CA3174208 A1 CA 3174208A1
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CA
Canada
Prior art keywords
quality score
data
quality
quality scores
sequence
Prior art date
Legal status (The legal status 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 status listed.)
Pending
Application number
CA3174208A
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English (en)
French (fr)
Inventor
Guillaume Alexandre Pascal RIZK
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Illumina Inc
Original Assignee
Illumina Inc
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 Illumina Inc filed Critical Illumina Inc
Publication of CA3174208A1 publication Critical patent/CA3174208A1/en
Pending legal-status Critical Current

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Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/50—Compression of genetic data
    • H—ELECTRICITY
    • H03—ELECTRONIC CIRCUITRY
    • H03M—CODING; DECODING; CODE CONVERSION IN GENERAL
    • H03M7/00—Conversion of a code where information is represented by a given sequence or number of digits to a code where the same, similar or subset of information is represented by a different sequence or number of digits
    • H03M7/30—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction
    • H03M7/3068—Precoding preceding compression, e.g. Burrows-Wheeler transformation
    • H03M7/3071—Prediction
    • H—ELECTRICITY
    • H03—ELECTRONIC CIRCUITRY
    • H03M—CODING; DECODING; CODE CONVERSION IN GENERAL
    • H03M7/00—Conversion of a code where information is represented by a given sequence or number of digits to a code where the same, similar or subset of information is represented by a different sequence or number of digits
    • H03M7/30—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction
    • H03M7/60—General implementation details not specific to a particular type of compression
    • H03M7/6011—Encoder aspects
    • H—ELECTRICITY
    • H03—ELECTRONIC CIRCUITRY
    • H03M—CODING; DECODING; CODE CONVERSION IN GENERAL
    • H03M7/00—Conversion of a code where information is represented by a given sequence or number of digits to a code where the same, similar or subset of information is represented by a different sequence or number of digits
    • H03M7/30—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction
    • H03M7/60—General implementation details not specific to a particular type of compression
    • H03M7/6017—Methods or arrangements to increase the throughput
    • H—ELECTRICITY
    • H03—ELECTRONIC CIRCUITRY
    • H03M—CODING; DECODING; CODE CONVERSION IN GENERAL
    • H03M7/00—Conversion of a code where information is represented by a given sequence or number of digits to a code where the same, similar or subset of information is represented by a different sequence or number of digits
    • H03M7/30—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction
    • H03M7/60—General implementation details not specific to a particular type of compression
    • H03M7/6017—Methods or arrangements to increase the throughput
    • H03M7/6029—Pipelining
    • H—ELECTRICITY
    • H03—ELECTRONIC CIRCUITRY
    • H03M—CODING; DECODING; CODE CONVERSION IN GENERAL
    • H03M7/00—Conversion of a code where information is represented by a given sequence or number of digits to a code where the same, similar or subset of information is represented by a different sequence or number of digits
    • H03M7/30—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction
    • H03M7/70—Type of the data to be coded, other than image and sound
    • H—ELECTRICITY
    • H03—ELECTRONIC CIRCUITRY
    • H03M—CODING; DECODING; CODE CONVERSION IN GENERAL
    • H03M7/00—Conversion of a code where information is represented by a given sequence or number of digits to a code where the same, similar or subset of information is represented by a different sequence or number of digits
    • H03M7/30—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction
    • H03M7/70—Type of the data to be coded, other than image and sound
    • H03M7/702—Software
    • H—ELECTRICITY
    • H03—ELECTRONIC CIRCUITRY
    • H03M—CODING; DECODING; CODE CONVERSION IN GENERAL
    • H03M7/00—Conversion of a code where information is represented by a given sequence or number of digits to a code where the same, similar or subset of information is represented by a different sequence or number of digits
    • H03M7/30—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction
    • H03M7/70—Type of the data to be coded, other than image and sound
    • H03M7/705—Unicode
    • H—ELECTRICITY
    • H03—ELECTRONIC CIRCUITRY
    • H03M—CODING; DECODING; CODE CONVERSION IN GENERAL
    • H03M7/00—Conversion of a code where information is represented by a given sequence or number of digits to a code where the same, similar or subset of information is represented by a different sequence or number of digits
    • H03M7/30—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction
    • H03M7/70—Type of the data to be coded, other than image and sound
    • H03M7/707—Structured documents, e.g. XML
    • H—ELECTRICITY
    • H03—ELECTRONIC CIRCUITRY
    • H03M—CODING; DECODING; CODE CONVERSION IN GENERAL
    • H03M7/00—Conversion of a code where information is represented by a given sequence or number of digits to a code where the same, similar or subset of information is represented by a different sequence or number of digits
    • H03M7/30—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction
    • H03M7/3084—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction using adaptive string matching, e.g. the Lempel-Ziv method
    • H—ELECTRICITY
    • H03—ELECTRONIC CIRCUITRY
    • H03M—CODING; DECODING; CODE CONVERSION IN GENERAL
    • H03M7/00—Conversion of a code where information is represented by a given sequence or number of digits to a code where the same, similar or subset of information is represented by a different sequence or number of digits
    • H03M7/30—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction
    • H03M7/40—Conversion to or from variable length codes, e.g. Shannon-Fano code, Huffman code, Morse code
    • H03M7/4006—Conversion to or from arithmetic code

Landscapes

  • Engineering & Computer Science (AREA)
  • Theoretical Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Biotechnology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biophysics (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioethics (AREA)
  • Databases & Information Systems (AREA)
  • Genetics & Genomics (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Compression, Expansion, Code Conversion, And Decoders (AREA)
  • Applications Or Details Of Rotary Compressors (AREA)
CA3174208A 2020-11-05 2021-11-05 Quality score compression Pending CA3174208A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US202063110308P 2020-11-05 2020-11-05
US63/110,308 2020-11-05
PCT/US2021/058364 WO2022099097A1 (en) 2020-11-05 2021-11-05 Quality score compression

Publications (1)

Publication Number Publication Date
CA3174208A1 true CA3174208A1 (en) 2022-05-12

Family

ID=78725748

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3174208A Pending CA3174208A1 (en) 2020-11-05 2021-11-05 Quality score compression

Country Status (12)

Country Link
US (4) US11527307B2 (https=)
EP (1) EP4241276A1 (https=)
JP (1) JP7810664B2 (https=)
KR (1) KR20230101760A (https=)
CN (1) CN115668384A (https=)
AU (1) AU2021376411A1 (https=)
BR (1) BR112022025042A2 (https=)
CA (1) CA3174208A1 (https=)
IL (2) IL298981B2 (https=)
MX (1) MX2022016020A (https=)
WO (1) WO2022099097A1 (https=)
ZA (2) ZA202304367B (https=)

Families Citing this family (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2022099097A1 (en) * 2020-11-05 2022-05-12 Illumina, Inc. Quality score compression
JP2022086403A (ja) * 2020-11-30 2022-06-09 キオクシア株式会社 メモリシステム及び情報処理システム
EP4490735A1 (en) 2022-03-08 2025-01-15 Illumina Inc Multi-pass software-accelerated genomic read mapping engine
US11775172B1 (en) * 2022-05-05 2023-10-03 CELLGENTEK Corp. Genome data compression and transmission method for FASTQ-formatted genome data
CN115662525B (zh) * 2022-10-25 2026-04-21 湖南大学 一种测序fastq文件质量分数序列的稀疏化处理方法

Family Cites Families (14)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20100205204A1 (en) 2007-03-02 2010-08-12 Research Organization Of Information And Systems Homology retrieval system, homology retrieval apparatus, and homology retrieval method
US10090857B2 (en) * 2010-04-26 2018-10-02 Samsung Electronics Co., Ltd. Method and apparatus for compressing genetic data
US20110288785A1 (en) * 2010-05-18 2011-11-24 Translational Genomics Research Institute (Tgen) Compression of genomic base and annotation data
AU2012272161B2 (en) * 2011-06-21 2015-12-24 Illumina Cambridge Limited Methods and systems for data analysis
US10777301B2 (en) * 2012-07-13 2020-09-15 Pacific Biosciences For California, Inc. Hierarchical genome assembly method using single long insert library
US10847251B2 (en) * 2013-01-17 2020-11-24 Illumina, Inc. Genomic infrastructure for on-site or cloud-based DNA and RNA processing and analysis
WO2014197377A2 (en) * 2013-06-03 2014-12-11 Good Start Genetics, Inc. Methods and systems for storing sequence read data
WO2016081712A1 (en) * 2014-11-19 2016-05-26 Bigdatabio, Llc Systems and methods for genomic manipulations and analysis
CN107851118A (zh) * 2015-05-21 2018-03-27 基因福米卡数据系统有限公司 下一代测序数据的存储、传输和压缩
JP6949970B2 (ja) 2016-10-11 2021-10-13 ゲノムシス エスアー バイオインフォマティクスデータを送信する方法及びシステム
CN110021349B (zh) * 2017-07-31 2021-02-02 北京哲源科技有限责任公司 基因数据的编码方法
CN110111852A (zh) * 2018-01-11 2019-08-09 广州明领基因科技有限公司 一种海量dna测序数据无损快速压缩平台
CN110797082A (zh) * 2019-10-24 2020-02-14 福建和瑞基因科技有限公司 基因测序数据的存储读取方法及系统
WO2022099097A1 (en) 2020-11-05 2022-05-12 Illumina, Inc. Quality score compression

Also Published As

Publication number Publication date
JP7810664B2 (ja) 2026-02-03
CN115668384A (zh) 2023-01-31
IL298981B2 (en) 2025-03-01
ZA202304367B (en) 2023-12-20
KR20230101760A (ko) 2023-07-06
IL316156B1 (en) 2026-04-01
IL298981A (en) 2023-02-01
WO2022099097A1 (en) 2022-05-12
ZA202402955B (en) 2025-04-30
BR112022025042A2 (pt) 2023-05-09
IL316156A (en) 2024-12-01
US20220139502A1 (en) 2022-05-05
US20240420804A1 (en) 2024-12-19
JP2023547973A (ja) 2023-11-15
MX2022016020A (es) 2023-02-02
US20230040143A1 (en) 2023-02-09
US12080385B2 (en) 2024-09-03
AU2021376411A1 (en) 2022-10-27
US20240062853A1 (en) 2024-02-22
US11527307B2 (en) 2022-12-13
IL298981B1 (en) 2024-11-01
EP4241276A1 (en) 2023-09-13
US11776663B2 (en) 2023-10-03

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