De novo genome assembly of NGS data VBC（门店数据VBC的新创基因组组装）.pdfVIP

De novo genome assembly of NGS data Dr Torsten Seemann Victorian Bioinformatics Consortium Monash University IMB Winter School 2011 IMB Winter School – Mathematical and Computational Biology Outline • Concepts – genome, read, graph, k-mer • Genome assembly – OLC and Eulerian method, software • Assembly metrics – N50 explained • If we have time… – simple example of running “Velvet” • Contact What is a genome? • The entire set of DNA that makes up a particular organism – Chromosomes – Organelles: mitochondria, chloroplast, ... – Plasmids – Viruses (some are RNA not DNA) – Bacteriophage • Essentially just a set of strings – Using the 4 letter DNA alphabet { A,G,C,T } Genome sizes • Virus, Plasmid, Phage – 1 kbp to 100 kbp … HIV 9181 bp • Bacteria, Archaea – 1 Mbp to 10 Mbp … E.coli 4.6 Mbp • Simple Eukaryotes – 10 Mbp to 100 Mbp … Malaria 23 Mbp • Animals, Plants – 100 Mbp to 100 Gbp ! … Human 3.2 Gbp Genome sequencing • Hierarchial (“Old School”) – Restriction frags, vectors, exo deletion, ... – Labour intensive but some advantages • Whole Genome Shotgun (“WGS”) – Shear DNA to appropriate size – Do some library preparation – Put in sequencing machine – Get some big text files with your reads – Panic when NOTEPAD.EXE won’t load them Genome assembly DNA copies Sequence Reads Assembled genome of the genome Previous talk This talk Read technologies Method bp Attributes Sanger