1前沿技术动态(高通量测序内部培训资料)

基因组学、生物信息学前沿技术动态BGI-ShenzhenOutlineIntroductionSequencingtechnologiesBioinformaticanalysisApplicationsTreeofLife(denovo)PopulationevolutionandBreeding(Resequencing)Disease(Resequencing)EpigenomicsTranscriptomicsMetagenomicsProteomicsGrowthofNCBI010,00020,00030,00040,00050,00060,000198219841986198819901992199419961998200020022004200620082010年份十亿碱基（Gb）GrowthofNCBIBGIisconstructingsupercomputingplatformtomatchtherequirementsSolutionforwetlabs：CloudcomputingCloudcomputingGenomeGenotypeMetabolomeEpigeneticsncRNAmRNAProteinPhenotypeFromgenotypetoPhenotype!GenotypeIntermediatePhenotypeMolecularPhenotypeOutlineIntroductionSequencingtechnologiesBioinformaticsanalysisApplicationsTreeofLife(denovo)PopulationevolutionandBreeding(Resequencing)Disease(Resequencing)EpigenomicsTranscriptomicsMetagenomicsProteomicsThefast-revolutionofDNAsequencingtechnologyListofavailabletehnologies:•3730,AB(Sangermethod)•454,Roche(Sequencing-by-Synthesis)•GenomeAnalyzer,HiSeq2000,illumina(Sequencing-by-Synthesis)•Solid,AB(Sequencing-by-ligation)•Helicos(thefirstSinglemolecularsequencing)Thefast-revolutionofDNAsequencingtechnologyPlantocommercializeinthisyear•PacBio,(Real-timesinglemolecularsequencing,longreads1-10kb)•visiGene,AB(Real-timesinglemolecularsequencing)•IonTorrent(Semiconductorchip,measuringpHchanging,quitelowprice)Start-developingtechnology(Nanopore,$100/genome)•Severalcompanies,includeillumina,IBM,etc.a.Sangersequencingmethodb.next-generationsequencingmethodOutlineIntroductionSequencingtechnologiesBioinformaticanalysisApplicationsTreeofLife(denovo)PopulationevolutionandBreeding(Resequencing)Disease(Resequencing)EpigenomeTranscriptomeMetagenomicsProteomicsPublishedBioinformaticsTools•BGIdevelopedsoftwarepackage•Website:•10,000usersSOAP-ShortOligonucleotideAlignmentProgramRelatedpublications•SOAP:RuiqiangLi,YingruiLi,KarstenKristiansen,JunWang.SOAP:shortoligonucleotidealignmentprogram.Bioinformatics.200824:713-714•SOAP2:RuiqiangLi,ChangYu,YingruiLi,Tak-WahLam,Siu-MingYiu,KarstenKristiansen,JunWang.SOAP2:animprovedultrafasttoolforshortreadalignment.Bioinformatics.2009•SOAPsnp:RuiqiangLi,YingruiLi,XiaodongFang,HuanmingYang,JianWang,KarstenKristiansen,JunWang.SNPdetectionformassivelyparallelwholegenomeresequencing.GenomeResearch.2009•SOAPindel,SOAPsv:iscoming…•SOAPdenovo:RuiqiangLi,HongmeiZhu,JueRuan,etal.Denovoassemblyofthehumangenomeswithmassivelyparallelshortreadsequencing.GenomeResearch.2009(1)SOAPalignerSingle-endreadsalignment25~60bpreadlengthUngappedandgappedalignmentUngappedhitshaveprecedenceovergappedhitsSince3’-endofreadexhibitamuchhighernumberofsequencingerrors,SOAPcaniterativelytrimlow-qualityreadendandredoalignmentuntilhitsaredetectedorremainingsequenceistooshortFormultipleequal-besthits,usercaninstructtheprogramtoreportnone,randomone,orallofthemPaired-endreadsalignmentAlignapairofreadssimultaneouslyApairwillbealignedwhentworeadsaremappedwiththerightorientationrelationshipandproperdistanceOutputunpairedhitsforstructuralvariation(SV)detectionBenchmark10Msingle-endIllumina/Solexareadswithlength32bpagainsta5Mbhumangenomeregion.(refertoSOAPpaperfordetails)(2)SOAPaligner2-AnimprovedversionImprovements:UseBurrowsWheelerTransformation(BWT)compressedindexinsteadoftheseedalgorithmNoreadlengthlimitationAllowmoremismatchesandlongergapsforlongreadsSupportvariousinputandoutputfileformatsInput:FASTA,FASTQ,gzippedOutput:SOAPtab-delimitedtable,SAM(sequencealignment/map),binaryequivalent(BAM),consedSOAP2:BenchmarkonhumandataFasterwithlessRAMusageHalfmemoryusagethanSOAP43and30timesfasterforsingle-endandpaired-endreads,respectively(3)SOAPsnp-SNPdetectionforshortreadsre-sequencingAlgorithm:SequencingreadsMapreadsontoreferencegenomeRecalibratesequencingqualityscoreCalculatelikelihoodofeachgenotypePriorprobabilityofeachgenotypeInferredgenotypeviaBayes’theoremUseBayes’theoremtoinferthegenotypegiventheobservedalleletypesandqualityscoresoneachchromosomalsite.SOAP(4)SOAPdenovoOutlineIntroductionSequencingtechnologiesBioinformaticanalysisApplicationsTreeofLife(denovo)PopulationevolutionandBreeding(Resequencing)Disease(Resequencing)EpigenomicsTranscriptomicsMetagenomicsProteomicsOutlineIntroductionSequencingtechnologiesBioinformaticanalysisApplicationsTreeofLife(denovo)PopulationevolutionandBreeding(Resequencing)Disease(Resequencing)EpigenomicsTranscriptomicsMetagenomicsProteomics一个物种基因组计划的完成，就意味着这一物种学科和产业发展的新开端。——向仲怀院士01002003004005006007001994199619982000200220042006200820102012ricewheat全基因组测序的发展1998200120022004200620072008200920102000基因组测序的时代已经来临全球基因组测序研究趋势FlowchartofSOAPdenovoPandaGenomeProject-NoteonIlluminawebsite.RuiqiangLi,WeiFan,et.al.Thecompletegenomesequenceofthegiantpanda.Nature.2009.PotatoGenomeProject组装统计备注：使用自主开发的SOAPdenovo软件，仅利用56X高质量的pair-end测序数据。Human,dog,pandacomparison蚂蚁种类基因组大小测序方法发表期刊发表时间印度跳蚁、佛罗里达弓背蚁弓240Mb印330MbIlluminaScience2010-8-27红火蚁352.7MbRoche454IlluminaPNAS2010-12-8红色收割蚁235MbRoche454PNAS2010-12-9阿根廷蚁215.6MbRoche454Il