CN115668384A - 质量分数压缩 - Google Patents

质量分数压缩 Download PDF

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Publication number
CN115668384A
CN115668384A CN202180039438.9A CN202180039438A CN115668384A CN 115668384 A CN115668384 A CN 115668384A CN 202180039438 A CN202180039438 A CN 202180039438A CN 115668384 A CN115668384 A CN 115668384A
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China
Prior art keywords
quality scores
data
quality
sequence
scores
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CN202180039438.9A
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English (en)
Chinese (zh)
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G·A·P·里兹克
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Inmair Ltd
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Inmair Ltd
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    • 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
    • H03M7/3084—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
    • 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

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  • 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)
CN202180039438.9A 2020-11-05 2021-11-05 质量分数压缩 Pending CN115668384A (zh)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US202063110308P 2020-11-05 2020-11-05
US63/110308 2020-11-05
PCT/US2021/058364 WO2022099097A1 (en) 2020-11-05 2021-11-05 Quality score compression

Publications (1)

Publication Number Publication Date
CN115668384A true CN115668384A (zh) 2023-01-31

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Country Status (12)

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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=)

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* 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

Citations (5)

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US20110288785A1 (en) * 2010-05-18 2011-11-24 Translational Genomics Research Institute (Tgen) Compression of genomic base and annotation data
US20130031092A1 (en) * 2010-04-26 2013-01-31 Samsung Electronics Co., Ltd. Method and apparatus for compressing genetic data
CN110021349A (zh) * 2017-07-31 2019-07-16 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

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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
WO2022099097A1 (en) 2020-11-05 2022-05-12 Illumina, Inc. Quality score compression

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US20130031092A1 (en) * 2010-04-26 2013-01-31 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
CN110021349A (zh) * 2017-07-31 2019-07-16 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

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RAYMOND WAN, ET AL.: "Transformations for the compression of FASTQ quality scores of next-generation sequencing data", 《BIOINFORMATICS》, vol. 28, no. 5, 1 March 2012 (2012-03-01), pages 628 - 635 *
陈惟昌, 陈志华, 陈志义, 王自强, 邱红霞: "遗传密码和DNA序列的高维空间数字编码", 生物物理学报, no. 04, 30 December 2000 (2000-12-30) *

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Publication number Publication date
JP7810664B2 (ja) 2026-02-03
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
CA3174208A1 (en) 2022-05-12
US11527307B2 (en) 2022-12-13
IL298981B1 (en) 2024-11-01
EP4241276A1 (en) 2023-09-13
US11776663B2 (en) 2023-10-03

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