BGI 动物案例研讨班课件：4-Genome assembly based on the Next-Gen sequencing technology.pdf

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1、GenomeassemblybasedontheNext-GensequencingtechnologyOUTLINEBackgroundRelationshipbetweensequencingandassemblyAssemblyalgorithmsintheNext-GensequencingHowmuchdatadoweneed?FactorsthataffectassemblyScaffoldextensionEvaluationoftheassemblyresult1998200020012002200420062007200820092010201120

2、11PublishedGenomesGenomealwaysbetheinitialunderstandingofaspeciericewheat7006005004003002001000OUTLINEBackgroundRelationshipbetweensequencingandassemblyAssemblyalgorithmsintheNext-GensequencingHowmuchdatadoweneed?FactorsthataffectassemblyScaffoldextensionEvaluationoftheassemblyresultWha

3、tisDNAsequencing?DNAsequencingistodeterminetheorderofthenucleotidebasesinamoleculeofDNA.Firstgenerationsequencer:Chain-terminationmethodsNextgenerationsequencer(Illumina/Roche):High-throughputsequencingThirdgenerationsequencer(PacBio/OpGen):SinglemoleculeChain-terminationmethodsDr.Fr

4、edSangerIlluminasequencing454sequencingMate-pairlibraryconstruction12ThedatacharacterofsolexaShortreadlength(current100bpforoneread)Highsequencingerror(~1%,highererrorrateonthe3’-end)Pair-endsequencingwithgradientinsertsizes:(170bp,500bp,800bp,2kb,5kb,10kb,20kb,40k)Thedataformatofill

5、uminaThedatacharacterof454Longreadlength(currentpeakreadlength~700bp,averagereadlength~500bp)HighsequencingerrorandsomeindelPair-endsequencingwithgradientinsertsizes:(1kb,2kb,3kb,8kb,20kb)Thedataformatof454Fastaformat:Basequality:Whatisgenomeassembly?Sequenceassemblyreferstoaligninga

6、ndmergingfragmentstoamuchlongerDNAsequenceinordertoreconstructtheoriginalsequence.Usingthereadfilestogetlongersequence.TwostrategiesAdvantageanddisadvantage•Hierarchicalshotgun–Complexandslowonexperimentstep–Easyoncomputationstep–Highcost,andhighquality–Usedonlybythehumangenomeproject•W

7、hole-genomeshotgun–Easyandfastonexperimentstep–Difficultoncomputationstep–Muchlowercost,andalittlelowerquality–UsedwidelybymanyothergenomeprojectsGenomeSequencingstrategyOUTLINEBackgroundRelationshipbetweensequencingandassemblyAssemblyalgorithmsintheNext-GensequencingHowmuchdat