Visualization-Simon

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1、Visualisationtoolsfornext-generationsequencingSimonAndersEBIisanOutstationoftheEuropeanMolecularBiologyLaboratory.Outline●Exploringandcheckingalignmentwithalignmentviewers●Usinggenomebrowsers●GettinganoverviewoverthewholedatawithHilbertcurvevisualization●Displayingpeaksalongside

2、featureannotationwiththe“GenomeGraph”packageAlignmentViewers:SAMtoolstviewHengLi(SangerInstitute)etal.Alignmentviewers:MaqViewJueRuan(BeijingGenomicsInstitute)etal.AlignmentViewer:MapViewHuaBao(SunYat-SenUniversity,Guangzhou)etal.SAMtoolspileupformatI       25514   G       G    

3、   42      0       25      5       ....^:.CCCCCI       25515   T       T       42      0       25      5       .....CC?CCI       25516   A       G       48      48      25      7       GGGGG^:G^:g     CCCCCC5I       25517   G       G       51      0       25      8       ......,

4、^:,      CCCCCC1?I       25518   T       T       60      0       25      11      ......,,^:.^:,^:,       CCCCCC3A<:;I       25519   T       T       60      0       25      11      ......,,.,,     CCCCCC>A@AAI       25520   G       G       60      0       25      11      ......,,

5、.,,     CCCACC>A@ACAAI       25523   A       A       72      0       25      15      ......,,.,,^:.

6、^:,^:,^:.   CCCCCC;ACAAC??CI       25524   C       C       72      0       25      15      ......,,.,,.,,. CCCCCC6<ACA?C=AC

7、      18      ......,,.,,.,,.,..  CCCCCC>ACAACAACACCI       25527   A       A       56      0       24      18      ......,,.,,.,,.,.G   CCCCCC?ACAA@A?CACCFields:chromosome,position,referencebase,consensusbase,consensusquality,SNPquality,maximummappingquality,coverage,basepile-u

8、p,basequalitypile-upCoveragevectors<--Solexarea