基因组组装技术课件

1、基因组组装 2019.10.29基因组组装 一、Genome survey Kmer: a continuous nucleic acid sequences, the length is K bp. Suppose the genome is unique to K, we can get G different kmers. when generate a read, the possibility of a certain kmer be sequenced is (L-K+1)/G. L/G is very small, the n_r is very large, this is o

2、bey to Poisson distribution. So,d_k = (L-K+1)/G*n_r n_k = (L-K+1)*n_rthen,G =n_k/d_k一、Genome survey Kmer: a conQuality control and filtering Reads having a N over 10% of its length. Reads from short insert-size libraries having more than 65% bases with the quality 7, and the reads from large insert-

3、size libraries that contained more than 80% bases with the quality 7. Read 1 and read 2 of two paired-end reads that were completely identical (and thus considered to be the products of PCR duplication).Quality control and filteringError correction before assemblyError correction before assemb二、SOAP

4、denovo 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

5、 pair-end reads二、SOAPdenovo algorithm SOAPdeSequence assembly refers to aligning and merging fragments to a much longer DNA sequence in order to reconstruct the original sequence.Overlap:contigGe+en+no+om+mi+ic+csGenomicsPair-end:scaffoldnomGenomesemassemblyGenome*assembly221、De bruijn graph constru

6、ctionSequence assembly refers to alReads : AGATCTTGTTATTGTTATTGATCTCCDe bruijn graph constructionliding to take Kmer from reads,storing the links betweenneighboring Kmers.If the Kmer is already existent,merge the links of it with the first ones.AGATCATCTTCTTGTTTGTTTGTTAGTTATATCTCTCTCCGATCTTCTTGTTATT

7、TATTGTTGATATTGATGATCReads : AGATCTTGTTATTGTTATTGATDe bruijn graphDe bruijn graph2、Graph simplification Contigs: GATCTTGTTATTGATCT GATCTCCAGATCTset -R parameterContigs: AGATCTTGTTATTGATCTCCRead1:AGATCTTGTTATT Read2:GTTATTGATCTCCAGATC 1GATCTATCTTGTTATTGATCATCTCC234AGATCGATCTATCTTTCTTGCTTGTTTGTTTGTTAGT

8、TATATCTCTCTCCTTATTTATTGATTGATTGATTGATC2、Graph simplification Contigs3、Pair-end mapping to contig3、Pair-end mapping to contig4、Construct scaffoldsNote:For mate-pair(=2Kb), the order is just opposite.A reliable link will be built between two contigs, when pair-end/mate-pair readssupport larger than th

9、e number be set.The gap size is estimated from the insert size of each reads pair.4、Construct scaffoldsNote:5、Gap closureGet reads located in the gap and then do local assembly.(1) Close gap by pair-end information (One end mapped on the contig, the other end fall in the gap)(2)Do a local assembly u

10、sing the reads fall in the gap to get a sequence connect with the both edges of two contigs.Note: Gap closure here also means extend contigs.5、Gap closureGet reads locatedSchematic overview Schematic overview 三、Evaluation of assembly resultLengthcontig (scaffold) N50 size, N90 size, total length, coverage ratio of genome.AccuracyCoverage of gene sequences, compare to EST or transcriptome sequences.Compare with golden standard (such as BAC/fosmid) .三、Evaluation of assembly resulEvaluation of Gene Region CoverageEvaluation of Gene Region CoveCompare with golden standardCompare with