IL309786A - Quality score calibration of BASECALLING systems - Google Patents

Quality score calibration of BASECALLING systems

Info

Publication number
IL309786A
IL309786A IL309786A IL30978623A IL309786A IL 309786 A IL309786 A IL 309786A IL 309786 A IL309786 A IL 309786A IL 30978623 A IL30978623 A IL 30978623A IL 309786 A IL309786 A IL 309786A
Authority
IL
Israel
Prior art keywords
sensor data
range
clusters
computer
subset
Prior art date
Application number
IL309786A
Other languages
English (en)
Hebrew (he)
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
Priority claimed from US17/839,387 external-priority patent/US20230029970A1/en
Application filed by Illumina Inc filed Critical Illumina Inc
Publication of IL309786A publication Critical patent/IL309786A/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
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/10—Signal processing, e.g. from mass spectrometry [MS] or from PCR
    • 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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/04—Architecture, e.g. interconnection topology
    • G06N3/045—Combinations of networks
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/04—Architecture, e.g. interconnection topology
    • G06N3/0464—Convolutional networks [CNN, ConvNet]
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/08—Learning methods
    • G06N3/084—Backpropagation, e.g. using gradient descent
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/08—Learning methods
    • G06N3/09—Supervised learning
    • 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
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20—Supervised data analysis

Landscapes

  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Data Mining & Analysis (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Computation (AREA)
  • Software Systems (AREA)
  • Artificial Intelligence (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • General Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Computing Systems (AREA)
  • Mathematical Physics (AREA)
  • General Physics & Mathematics (AREA)
  • Computational Linguistics (AREA)
  • Biomedical Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Analytical Chemistry (AREA)
  • Bioethics (AREA)
  • Public Health (AREA)
  • Organic Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Signal Processing (AREA)
  • Biochemistry (AREA)
  • Genetics & Genomics (AREA)
IL309786A 2021-07-28 2022-07-28 Quality score calibration of BASECALLING systems IL309786A (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US202163226707P 2021-07-28 2021-07-28
US17/839,387 US20230029970A1 (en) 2021-07-28 2022-06-13 Quality score calibration of basecalling systems
PCT/US2022/038729 WO2023009758A1 (fr) 2021-07-28 2022-07-28 Étalonnage de score de qualité de systèmes d'appel de bases

Publications (1)

Publication Number Publication Date
IL309786A true IL309786A (en) 2024-02-01

Family

ID=83149575

Family Applications (1)

Application Number Title Priority Date Filing Date
IL309786A IL309786A (en) 2021-07-28 2022-07-28 Quality score calibration of BASECALLING systems

Country Status (6)

Country Link
EP (1) EP4377960A1 (fr)
KR (1) KR20240037882A (fr)
AU (1) AU2022319125A1 (fr)
CA (1) CA3223746A1 (fr)
IL (1) IL309786A (fr)
WO (1) WO2023009758A1 (fr)

Family Cites Families (32)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA2044616A1 (fr) 1989-10-26 1991-04-27 Roger Y. Tsien Sequencage de l'adn
US5641658A (en) 1994-08-03 1997-06-24 Mosaic Technologies, Inc. Method for performing amplification of nucleic acid with two primers bound to a single solid support
US6090592A (en) 1994-08-03 2000-07-18 Mosaic Technologies, Inc. Method for performing amplification of nucleic acid on supports
WO1998044152A1 (fr) 1997-04-01 1998-10-08 Glaxo Group Limited Methode de sequençage d'acide nucleique
ATE545710T1 (de) 1997-04-01 2012-03-15 Illumina Cambridge Ltd Verfahren zur vervielfältigung von nukleinsäuren
AR021833A1 (es) 1998-09-30 2002-08-07 Applied Research Systems Metodos de amplificacion y secuenciacion de acido nucleico
US20020150909A1 (en) 1999-02-09 2002-10-17 Stuelpnagel John R. Automated information processing in randomly ordered arrays
CN101525660A (zh) 2000-07-07 2009-09-09 维西根生物技术公司 实时序列测定
US7211414B2 (en) 2000-12-01 2007-05-01 Visigen Biotechnologies, Inc. Enzymatic nucleic acid synthesis: compositions and methods for altering monomer incorporation fidelity
AR031640A1 (es) 2000-12-08 2003-09-24 Applied Research Systems Amplificacion isotermica de acidos nucleicos en un soporte solido
US7057026B2 (en) 2001-12-04 2006-06-06 Solexa Limited Labelled nucleotides
US20040002090A1 (en) 2002-03-05 2004-01-01 Pascal Mayer Methods for detecting genome-wide sequence variations associated with a phenotype
ES2326077T3 (es) 2002-08-23 2009-09-30 Illumina Cambridge Limited Nucleotidos marcados.
DK3363809T3 (da) 2002-08-23 2020-05-04 Illumina Cambridge Ltd Modificerede nukleotider til polynukleotidsekvensering
GB0321306D0 (en) 2003-09-11 2003-10-15 Solexa Ltd Modified polymerases for improved incorporation of nucleotide analogues
EP1701785A1 (fr) 2004-01-07 2006-09-20 Solexa Ltd. Reseaux moleculaires modifies
CA2579150C (fr) 2004-09-17 2014-11-25 Pacific Biosciences Of California, Inc. Appareil et procede d'analyse de molecules
EP1828412B2 (fr) 2004-12-13 2019-01-09 Illumina Cambridge Limited Procede ameliore de detection de nucleotides
WO2006120433A1 (fr) 2005-05-10 2006-11-16 Solexa Limited Polymerases ameliorees
US8045998B2 (en) 2005-06-08 2011-10-25 Cisco Technology, Inc. Method and system for communicating using position information
GB0514936D0 (en) 2005-07-20 2005-08-24 Solexa Ltd Preparation of templates for nucleic acid sequencing
GB0517097D0 (en) 2005-08-19 2005-09-28 Solexa Ltd Modified nucleosides and nucleotides and uses thereof
US7405281B2 (en) 2005-09-29 2008-07-29 Pacific Biosciences Of California, Inc. Fluorescent nucleotide analogs and uses therefor
GB0522310D0 (en) 2005-11-01 2005-12-07 Solexa Ltd Methods of preparing libraries of template polynucleotides
WO2007107710A1 (fr) 2006-03-17 2007-09-27 Solexa Limited Procédés isothermiques pour créer des réseaux moléculaires clonales simples
EP3373174A1 (fr) 2006-03-31 2018-09-12 Illumina, Inc. Systèmes et procédés pour analyse de séquençage par synthèse
US20080242560A1 (en) 2006-11-21 2008-10-02 Gunderson Kevin L Methods for generating amplified nucleic acid arrays
US7595882B1 (en) 2008-04-14 2009-09-29 Geneal Electric Company Hollow-core waveguide-based raman systems and methods
US9453258B2 (en) 2011-09-23 2016-09-27 Illumina, Inc. Methods and compositions for nucleic acid sequencing
US20160110499A1 (en) * 2014-10-21 2016-04-21 Life Technologies Corporation Methods, systems, and computer-readable media for blind deconvolution dephasing of nucleic acid sequencing data
WO2019147904A1 (fr) * 2018-01-26 2019-08-01 Quantum-Si Incorporated Appel de bases et d'impulsions activé par apprentissage automatique pour dispositifs de séquençage
US11347965B2 (en) * 2019-03-21 2022-05-31 Illumina, Inc. Training data generation for artificial intelligence-based sequencing

Also Published As

Publication number Publication date
KR20240037882A (ko) 2024-03-22
CA3223746A1 (fr) 2023-02-02
AU2022319125A1 (en) 2024-01-18
EP4377960A1 (fr) 2024-06-05
WO2023009758A1 (fr) 2023-02-02

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