基因测序与组装解说.ppt

OUTLINE DNA sequencing Genome Assembly 2012 Published Genomes What is DNA sequencing? DNA sequencing is to determine the order of the nucleotide bases in a molecule of DNA. First generation sequencer: Chain-termination methods Next generation sequencer(Illumina/Roche): High-throughput sequencing Third generation sequencer(PacBio): Single molecule Chain-termination methods Chain-termination methods Illumina sequencing 454 sequencing What is genome assembly? Sequence assembly refers to aligning and merging fragments to a much longer DNA sequence in order to reconstruct the original sequence. Using the read files to get longer sequence. Why do assemble ? sanger测序：500～1000bp ? Illumina测序：200-500bp ? pacific ：10kbp ? 人的基因组大小为3Gbp How to assemble? 很长的毕业照是怎么拍的呢？ ? 寻找reads之间的overlap ATACCTTGCTAGCGT GCTAGCGTAGGTCTGA =ATACCTTGCTAGCGTAGGTCTGA genome assembly In shotgun sequencing,DNA is broken up randomly into numerous small segments.Multiple overlapping reads for the target DNA are obtained by performing several rounds of this fragmentation and sequencing. Computer programs then use the overlapping ends of different reads to assemble them into a continuous sequence. Two strategies Advantage and disadvantage Hierarchical shotgun Complex and slow on experiment step High cost, and high quality Used only by the human genome project Whole-genome shotgun Easy and fast on experiment step Much lower cost, and a little lower quality Used widely by many other genome projects Sequence assembly Sequence assembly refers to aligning and merging fragments to a much longer DNA sequence in order to reconstruct the original sequence. Overlap: contig Ge+en+no+om+mi+ic+cs ? Genomics Pair-end: scaffold nom sem ? Genome****assembly Genome assembly De Bruijn Graph The most common used algorithm for short-read (illumina, Solid) assembly, also called kmer g