11/14/13 1 2013 ( BMMB 597D: Analyzing Next Genera>on Sequencing Data Week 12, Lecture 24 István Albert Biochemistry and Molecular Biology and Bioinforma>cs Consul>ng Center Penn State Topics to be covered in the next lectures 1. Assembly – building new genomes/ transcriptomes 2. Metagenomics – characterizing mul>ple genomes 3. Chip<Seq – quan>fying loca>ons in genomes 4. RNA<Seq – quan>fying gene expressions Genome Assembly The path to a whole genome Mul>step process 1. Assemble short reads into longer sequences ! conBgs 2. Scaffolding – arrange con>gs rela>ve to one another based on external informa>on 3. Genome finishing (gap closure) ! fill in gaps with directed sequencing procedures and manual cura>on AMOS – A Modular Open(Source whole genome assembler It is not a single so[ware rather than a collec>on of interoperable tools, standards and techniques
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