IL298981B2 - Compression quality score - Google Patents

Compression quality score

Info

Publication number
IL298981B2
IL298981B2 IL298981A IL29898122A IL298981B2 IL 298981 B2 IL298981 B2 IL 298981B2 IL 298981 A IL298981 A IL 298981A IL 29898122 A IL29898122 A IL 29898122A IL 298981 B2 IL298981 B2 IL 298981B2
Authority
IL
Israel
Prior art keywords
quality scores
sequence
quality
data
quality score
Prior art date
Application number
IL298981A
Other languages
English (en)
Hebrew (he)
Other versions
IL298981A (en
IL298981B1 (en
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 IL298981A publication Critical patent/IL298981A/en
Publication of IL298981B1 publication Critical patent/IL298981B1/en
Publication of IL298981B2 publication Critical patent/IL298981B2/en

Links

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
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/50—Compression of genetic data
    • 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
    • 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

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)
IL298981A 2020-11-05 2021-11-05 Compression quality score IL298981B2 (en)

Applications Claiming Priority (2)

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

Publications (3)

Publication Number Publication Date
IL298981A IL298981A (en) 2023-02-01
IL298981B1 IL298981B1 (en) 2024-11-01
IL298981B2 true IL298981B2 (en) 2025-03-01

Family

ID=78725748

Family Applications (2)

Application Number Title Priority Date Filing Date
IL298981A IL298981B2 (en) 2020-11-05 2021-11-05 Compression quality score
IL316156A IL316156B1 (en) 2020-11-05 2021-11-05 Compression quality score

Family Applications After (1)

Application Number Title Priority Date Filing Date
IL316156A IL316156B1 (en) 2020-11-05 2021-11-05 Compression quality score

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
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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