基因组组装技术课件

Click to edit Master title style,Click to edit Master text styles,Second level,Third level,Fourth level,Fifth level,11/7/2009,#,单击此处编辑母版标题样式,单击此处编辑母版文本样式,第二级,第三级,第四级,第五级,*,基因组组装,2019.10.29,基因组组装,一,、,Genome survey,Kmer:,a,c,o,ntinuous,nu,c,leic,a,c,id,s,e,que,n,c,e,s,the,length,is K,bp.,Suppo,s,e,the,gen,o,me,is,unique,to,K,we can,get,G,di,f,ferent,kmer,s,.,when,gen,e,rate,a,read,the,po,s,sibili,t,y,of,a,c,e,rtain,kmer,be s,e,que,n,c,e,d,is,(L-K+1,),/,G.,L/G,is,v,ery,small,the,n_r,is,v,ery,large,th,i,s,is obey,to,P,ois,s,on,distribution,.,So,d_k,=,(,L,-K+1,),/,G,*,n_r n_k,=,(,L,-K+1,),*,n_r,then,G,=,n,_,k,/,d_k,一、Genome survey Kmer:a con,Quality,c,o,n,t,r,ol and,fil,t,ering,R,eads,h,a,ving,a,N,o,v,er,1,0,%,of its,len,g,th.,R,e,a,ds,f,r,om,sh,ort inser,t,-,si,z,e,lib,r,ari,e,s,h,a,ving,mo,r,e than 6,5,%bases with,the quality,7,and the,r,eads f,r,om la,r,g,e,inser,t,-,si,z,e lib,r,ari,e,s th,a,t,c,o,n,t,ained mo,r,e,than 8,0,%,bases,with,the,quality,7.,R,e,a,d,1,and,r,e,a,d,2,of,t,w,o,pai,r,e,d-,end,r,e,a,ds,th,a,t,w,e,r,e,c,ompl,e,t,ely ide,n,ti,c,al,(and,thus,c,o,n,side,r,ed,t,o,be the,p,r,o,d,ucts,o,f,P,CR dupli,c,a,tion).,Quality control and filtering,Error corre,c,tion,before,as,s,emb,l,y,Error correction before assemb,二、,SOAPdenovo,algorithm,SOAPdenovo was developed to assemble,large genomes,such as human,it also works well for small genomes like bacteria.,Include five major steps:,De bruijn graph construction,Graph simplification and obtain contigs,Pair-end reads mapping to contigs,Construct scaffolds,Gap filling with pair-end reads,二、SOAPdenovo algorithm SOAPde,S,e,q,u,e,n,ce,ass,e,mb,l,y,ref,e,rs,t,o,a,l,i,g,n,i,ng,a,n,d m,e,rg,i,ng,fra,g,me,n,ts,to a much l,o,n,g,er,D,N,A,se,q,u,e,nce,in,or,d,er,to rec,o,nstr,u,ct,the,ori,g,i,n,al,se,q,u,e,nc,e,.,Overl,a,p:,co,n,tig,G,e,+,e,n,+,n,o,+,o,m,+,m,i,+,i,c,+,c,s,G,e,n,o,m,i,c,s,P,a,i,r,-,end:,sca,f,fold,nom,Ge,no,m,e,s,e,m,a,s,s,e,m,bly,Genome*,*,*,a,sse,m,bly,22,1,、,De bruijn,g,r,aph,c,o,n,s,truction,Sequence assembly refers to al,R,e,ads,:,A,G,A,TC,T,T,GT,T,A,TT,GT,T,A,T,T,G,A,TCT,CC,De bruijn,g,r,aph,c,o,n,s,truction,l,id,i,n,g,to,take,Km,e,r fr,o,m re,a,d,s,stor,in,g,the,li,n,ks,be,t,w,ee,n,n,e,i,g,h,b,or,i,ng,Kmers.,If,the,Kmer is a,l,re,a,dy,e,x,iste,n,t,mer,g,e,the,li,n,ks,of it,w,ith,the first,o,n,e,s.,A,G,A,T,C,A,TCT,T,CTT,GT,TT,G,T,T,T,G,T,T,A,G,T,T,A,T,A,TCT,C,TCTCC,G,A,TC,T,TCTTG,T,T,A,T,T,T,A,TT,G,TT,G,A,T,A,TT,G,A,T,G,A,T,C,Reads:AGATCTTGTTATTGTTATTGAT,De,bruijn,g,r,aph,De bruijn graph,2,、,Graph,simpl,i,ficat,i,on,C,o,nti,g,s:,G,A,T,C,T,T,G,T,TA,T,T,G,A,TCT G,A,T,C,T,CC,A,G,A,T,CT,s,e,t,-,R,pa,r,a,m,e,ter,C,o,nti,g,s:,A,G,A,T,C,T,T,G,T,T,A,TT,G,A,TC,T,CC,R,e,ad,1,:,A,G,A,TC,T,T,G,T,T,A,TT,R,e,ad2,:,G,T,T,A,T,T,G,A,T,C,T,CC,A,G,A,T,C,1,G,A,TC,T,A,TCT,T,GT,T,A,TT,G,A,T,C,A,TCTC,C,2,3,4,A,G,A,T,C,G,A,TC,T,A,TCT,T,TCTTG,CTT,GT,TT,G,T,T,T,G,T,T,A,G,T,T,A,T,A,TCT,C,TCTCC,T,T,A,T,T,T,A,TT,G,A,TT,G,A,TT,G,A,T,T,G,A,T,C,2、Graph simplification Contigs,3,、,P,ai,r-,end,mapping,t,o,c,o,n,tig,3、Pair-end mapping to contig,4,、,C,o,n,s,truct s,c,a,f,f,olds,N,o,te:,For mat,e,-p,a,ir(,=,2,K,b),t,he,or,d,er,is j,u,st,o,p,p,o,site.,A,r,e,l,iab,le,l,in,k,w,i,l,l,b,e,b,u,i,l,t,be,t,w,ee,n,t,w,o,c,on,ti,g,s,w,he,n,pa,i,r-,end,/mat,e,-,pa,ir,r,ead,s,su,p,p,o,rt,l,a,rg,e,r,th,a,n the,n,u,mb,e,r,be,set.,T,he,g,a,p,size,is estim,a,ted,from,the,ins,e,rt,size,of e,a,ch r,e,a,d,s,p,a,i,r,.,4、Construct scaffoldsNote:,5,、,Gap,c,los,u,r,e,Get,re,ads,loca,t,e,d,in,the,gap,and,then,do,loca,l,a,s,s,embl,y,.,(1)C,l,ose,g,a,p,by,p,a,ir-e,n,d,i,n,formati,o,n,(One,e,n,d m,a,p,p,ed,on the,co,n,tig,the,oth,e,r,e,n,d fa,l,l,in,t,he,g,a,p),(2),D,o,a l,o,cal,ass,e,mb,l,y,us,i,ng,the,re,a,ds fa,l,l,in,t,he,g,a,p,to,g,e,t,a se,q,u,e,nce,co,n,n,e,ct,w,ith,the,b,o,th e,d,g,e,s,of t,w,o,co,n,tig,s,.,N,o,te:Gap,clos,u,re,h,e,re,a,l,so m,e,a,n,s,e,x,te,n,d,co,n,tig,s,.,5、Gap closureGet reads located,S,c,he,m,at,i,c,o,v,erv,iew,Schematic overview,三、,E,v,alu,a,tion,o,f ass,e,mbly,r,es,u,lt,Le,n,gth,contig,(sca,f,fold),N,5,0,siz,e,N,9,0,siz,e,total le,n,gth,coverage,ratio of ge,n,ome.,A,c,c,u,racy,C,o,verage,of,g,ene,seq,u,enc,e,s,compare,t,o,E,S,T,or t,r,anscriptome,seq,u,enc,e,s.,C,o,mpare,w,i,th,go,l,den,standard(such as,B,A,C,/,fosmi,d,),.,三、Evaluation of assembly resul,E,v,alu,a,tion,of Gene,R,egion,C,o,v,e,r,a,g,e,Evaluation of Gene Region Cove,C,o,mpa,r,e w,i,th,g,olden,st,an,d,a,r,d,Compare with golden standard,Comparative genomic analysis,Comparative genomic analysis,Accu,r,acy of,g,ene,s,truct,u,r,es,Accuracy of gene structures,Than,k,y,o,u,f,o,r,l,istening,!,Thank you for listening!,