Genome assembly strategies – yesterday, today and tomorrow – Thorsten Seemann

De novo assembly is the process of reconstructing a genome’s DNA sequence using only a set of much shorter error-prone sequences (reads) sampled from the genome. A good metaphor is to take a newspaper, make twenty photocopies, shred them all, and then try to reconstruct the original newspaper – somewhat challenging. This presentation will discuss the principles of de novo assembly, the classical algorithmic approaches used for first-generation sequence data (Sanger), the current approaches for second-generation sequence data (Illumina/SOLiD/454), and a discussion of needs for upcoming technologies. Practical Issues of computational and memory requirements, assembly terminology, naming and file formats, available software, and an example run-through of an assembly using the Velvet software will be covered.


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