SAV Sequencing Analysis Viewer )での SAV(Sequencing Analysis Viewer)とは? ランの状況をモニターしたりランのクオリティを評価するためのソフトウェア」です。 配列情報などを参照するためのものではあ

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  • 2012 Illumina, Inc. All rights reserved.

    Illumina, illuminaDx, BaseSpace, BeadArray, BeadXpress, cBot, CSPro, DASL, DesignStudio, Eco, GAIIx, Genetic Energy, Genome Analyzer, GenomeStudio, GoldenGate, HiScan, HiSeq, Infinium,

    iSelect, MiSeq, Nextera, Sentrix, SeqMonitor, Solexa, TruSeq, VeraCode, the pumpkin orange color, and the Genetic Energy streaming bases design are trademarks or registered trademarks of

    Illumina, Inc. All other brands and names contained herein are the property of their respective owners.

    SAVSequencing Analysis ViewerRun

    Sep 18, 2015

  • 2

    SAVSequencing Analysis Viewer

  • 3

    SAV

    SAVPC

    http://support.illumina.com/sequencing/sequencing_software/sequencing_analy

    sis_viewer_sav.html

    SAV v1.9.1.Net Framework 4.5PC

    http://support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav.htmlhttp://support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav.htmlhttp://support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav.html

  • 4

    SAV

    Run folder

    InterOp folder

    runParameters.xml

    RunInfo.xml

  • 5

    RunSAV

    Run folderpathRefresh

  • 6

    SAV

    MiSeq NextSeq

    HiSeq

    Rapid

    Run

    HiSeq

    High

    Output

  • 7

    Q30

    Passing FilterPF

    Phasing/Prephasing

    FWHM

  • 8

    Q30

    Passing FilterPF

    Phasing/Prephasing

    FWHM

  • 9

    Q30

    Q Score = Phread

    Q30Q30

    Phred

    Quality Score

    Q-

    score

    10 1 in 10 90% Q10

    20 1 in 100 99% Q20

    30 1 in 1000 99.9% Q30

    40 1 in 10000 99.99% Q40

    Understanding Quality Score:

    http://support.illumina.com/content/dam/illumina-

    marketing/documents/products/technotes/technote_understanding_quality_scores.pdf

    Quality Scores for Next-Generation Sequencing

    http://www.illumina.com/documents/products/technotes/technote_Q-Scores.pdf

    http://support.illumina.com/content/dam/illumina-marketing/documents/products/technotes/technote_understanding_quality_scores.pdfhttp://support.illumina.com/content/dam/illumina-marketing/documents/products/technotes/technote_understanding_quality_scores.pdfhttp://support.illumina.com/content/dam/illumina-marketing/documents/products/technotes/technote_understanding_quality_scores.pdfhttp://support.illumina.com/content/dam/illumina-marketing/documents/products/technotes/technote_understanding_quality_scores.pdfhttp://www.illumina.com/documents/products/technotes/technote_Q-Scores.pdfhttp://www.illumina.com/documents/products/technotes/technote_Q-Scores.pdfhttp://www.illumina.com/documents/products/technotes/technote_Q-Scores.pdfhttp://www.illumina.com/documents/products/technotes/technote_Q-Scores.pdf

  • 10

    AnalysisQScore Distribution

  • 11

    AnalysisData By Cycle

  • 12

    Summary

  • 13

    %>=Q30 PhiX 2x50bp 2x75bp 2x100bp 2x125bp 2x150bp 2x250bp 2x300bp

    GAIIx 85%

    N/A

    80%

    N/A

    N/A

    N/A

    N/A

    HiSeq

    HO SBS

    V3

    85%

    N/A

    80%

    N/A

    N/A

    N/A

    N/A

    HiSeq

    HO SBS

    V4

    85% N/A

    80%

    80%

    N/A

    N/A

    N/A

    HiSeq

    Rapid Run 85%

    N/A

    80%

    N/A

    N/A

    75%

    N/A

    NextSeq N/A 80% N/A N/A 75% N/A N/A

    MiSeq V2 N/A N/A N/A N/A 80% 75% N/A

    MiSeq V3 N/A

    85%

    N/A

    N/A

    N/A N/A 70%

  • 14

    15-

    https://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-

    concentrations-for-verification-runs

    PhiX

    15-20

    https://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runs

  • 15

    16S metagenome amplicon

    PhiX

    Low Diversity2013/12/6

    http://www.illuminakk.co.jp/documents/pdf/2013_illumina_techsupport_session28.pdf

    16S rRNA 2014/5/9

    http://www.illuminakk.co.jp/documents/pdf/2014_techsupport_session3.pdf

    http://www.illuminakk.co.jp/documents/pdf/2013_illumina_techsupport_session28.pdfhttp://www.illuminakk.co.jp/documents/pdf/2013_illumina_techsupport_session28.pdfhttp://www.illuminakk.co.jp/documents/pdf/2014_techsupport_session3.pdfhttp://www.illuminakk.co.jp/documents/pdf/2014_techsupport_session3.pdf

  • 16

    Q30

    Cluster Passing FilterPF

    Phasing/Prephasing

    FWHM

  • 17

    Q Score

    PhiX

    https://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phi

    x-loading-concentrations-for-verification-runs

    Cluster Passing Filter (% Cluster PF

    Cluster Pass Filter2013/11/15

    http://www.illuminakk.co.jp/documents/pdf/2013_techsupport_session27.pdf

    Cluster PF

    https://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttps://my.illumina.com/MyIllumina/Bulletin/u2a5_szu_U6m0GkgddS6Vg/phix-loading-concentrations-for-verification-runshttp://www.illuminakk.co.jp/documents/pdf/2013_techsupport_session27.pdfhttp://www.illuminakk.co.jp/documents/pdf/2013_techsupport_session27.pdf

  • 18

    AnalysisData by Lane

  • 19

    Summary

  • 20

    images

  • 21

    S/N

    MiSeq2014/7/25

    http://www.illuminakk.co.jp/documents/pdf/2014_techsupport_session8.pdf

    http://www.illuminakk.co.jp/documents/pdf/2014_techsupport_session8.pdfhttp://www.illuminakk.co.jp/documents/pdf/2014_techsupport_session8.pdf

  • 22

    MiSeqTech note

    https://support.illumina.com/content/dam/illumina-

    marketing/documents/products/other/miseq-overclustering-primer-770-2014-038.pdf

    https://support.illumina.com/content/dam/illumina-marketing/documents/products/other/miseq-overclustering-primer-770-2014-038.pdfhttps://support.illumina.com/content/dam/illumina-marketing/documents/products/other/miseq-overclustering-primer-770-2014-038.pdfhttps://support.illumina.com/content/dam/illumina-marketing/documents/products/other/miseq-overclustering-primer-770-2014-038.pdfhttps://support.illumina.com/content/dam/illumina-marketing/documents/products/other/miseq-overclustering-primer-770-2014-038.pdfhttps://support.illumina.com/content/dam/illumina-marketing/documents/products/other/miseq-overclustering-primer-770-2014-038.pdfhttps://support.illumina.com/content/dam/illumina-marketing/documents/products/other/miseq-overclustering-primer-770-2014-038.pdfhttps://support.illumina.com/content/dam/illumina-marketing/documents/products/other/miseq-overclustering-primer-770-2014-038.pdfhttps://support.illumina.com/content/dam/illumina-marketing/documents/products/other/miseq-overclustering-primer-770-2014-038.pdfhttps://support.illumina.com/content/dam/illumina-marketing/documents/products/other/miseq-overclustering-primer-770-2014-038.pdfhttps://support.illumina.com/content/dam/illumina-marketing/documents/products/other/miseq-overclustering-primer-770-2014-038.pdfhttps://support.illumina.com/content/dam/illumina-marketing/documents/products/other/miseq-overclustering-primer-770-2014-038.pdfhttps://support.illumina.com/content/dam/illumina-marketing/documents/products/other/miseq-overclustering-primer-770-2014-038.pdfhttps://support.illumina.com/content/dam/illumina-marketing/documents/products/other/miseq-overclustering-primer-770-2014-038.pdfhttps://support.illumina.com/content/dam/illumina-marketing/documents/products/other/miseq-overclustering-primer-770-2014-038.pdf

  • 23

    Q30

    Cluster Passing FilterPF

    Phasing/Prephasing

    FWHM

  • 24

    Phasing/Prephasing

    Sequencing

    Phasing Prephasing

    A A

    G C C C C C

    DNA DNA DNA

    5 3

    3

    5

    1

  • 25

    Phasing/Prephasing

    Phasing/Prephasing~0.5%

    PhasingPrepasingDelivery

    Wash

    FCReagent Chiller

  • 26

    Summary

  • 27

    Q30

    Cluster Passing FilterPF

    Phasing/Prephasing

    FWHM

  • 28

    FWHM

    FWHM: Full Width Half Max

    Intensity

  • 29

    AnalysisData By Cycle

  • 30

    FWHM FWHM: Full Width Half Max

    24

    FWHM FWHM

  • 31

  • 32

    Case 1MiSeq V3 300PE run

    9Intensity

    Q score

  • 33

    Case 1MiSeq V3 300 PE run

    Cluster DensityMiSeq v3~1400K/mm2

    PFQ score

  • 34

    Case 1MiSeq V3 300 PE run

    Intensity

  • 35

    Case 2HiSeq V3 High Output100PE run

    Read2Intensity

    PFQ score

  • 36

    Case 2HiSeq V3 High Output100PE run

    Q score>=Q30Read1Read2

  • 37

    Case 3HiSeq V3 High OutputPE run

    HiSeq V3 High Output750 ~ 850K/mm2

    Read2Q score

    Read1

  • 38

    Case 3MiSeq V2 250 PE run

    Intensity

    PFQ score

  • 39

    Case 3MiSeq V2 250 PE run

    T A C G C A G C A G T Whole Genome Sample

  • 40

    Case 3MiSeq V2 250 PE run

    MiSeq1000K/mm2Q score

    MCS v2.3800K/mm25~20%PhiX

    16S rRNA 2014/5/9

    http://www.illuminakk.co.jp/documents/pdf/2014_techsupport_session3.pdf

    http://www.illuminakk.co.jp/documents/pdf/2014_techsupport_session3.pdf

  • 41

    SAV

    http://support.illumina.com/sequencing/sequencing_softwa

    re/sequencing_analysis_viewer_sav.ilmn

    Sequencing Analysis Viewer (SAV) User Guide

    https://support.illumina.com/downloads/sequencing_analys

    is_viewer_user_guide_15020619.html

    TechSupport BulletinMyillumina https://my.illumina.com/Home/Index

    http://support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav.ilmnhttp://support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav.ilmnhttp://support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav.ilmnhttp://support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav.ilmnhttps://support.illumina.com/downloads/sequencing_analysis_viewer_user_guide_15020619.htmlhttps://support.illumina.com/downloads/sequencing_analysis_viewer_user_guide_15020619.htmlhttps://support.illumina.com/downloads/sequencing_analysis_viewer_user_guide_15020619.htmlhttps://support.illumina.com/downloads/sequencing_analysis_viewer_user_guide_15020619.htmlhttps://my.illumina.com/Home/Indexhttps://my.illumina.com/Home/Indexhttps://my.illumina.com/Home/Index

  • 42

    !

    techsupport@illumina.com

    mailto:techsupport@illumina.com

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