De novo genome assembly – Torsten 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. It is the “original” genomics ‐ based bioinformatics problem, because it is all we can do when we don’t have any related reference genome sequences, with the exemplar being the human genome project. This presentation will discuss the principles of and approaches to de novo assembly of data from the current NGS platforms (Illumina, SOLiD, 454, IonTorrent, PacBio), and briefly cover upcoming technologies. Other practical issues covered will be of computational and memory requirements, limitations of de novo assembly, terminology, file formats, available software, and an example run ‐ through of an assembly using the Velvet software if time permits.

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