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Speaker: Leena Salmela (3.15pm-4pm)

Title: Optical mapping data: from raw data to genome assembly

Abstract: Optical maps are produced by immobilising ensembles of DNA molecules on a plate and applying a restriction enzyme to cut or nick the DNA molecules at a specific DNA motif. The molecules are then imaged and the cutting sites can be read from the image thus capturing the relative order and size of fragments between the cut sites. This process produces raw optical mapping data called Rmaps which are sequences of fragment sizes. Rmaps are hundreds of thousands of bases long with a high error level. Optical
mapping data can be used together with high-throughput sequencing to investigate a genome. In this talk I will give an overview of our recent research on developing methods for Rmaps and genome-wide optical maps. First, we have developed methods to reduce the error level or the raw data which helps in the downstream analysis. Secondly, we have studied finding overlaps between Rmaps which is the first step in assembling Rmaps to genome wide optical maps. As an alternative strategy, we have studied aligning the Rmaps directly to an assembly graph. Finally, we have developed a method for improving contig assembly with a genome-wide optical map.


Coffee, tea and cookies (4pm-4.30pm)


Speaker: Kimmo Palin (4.30pm – 5pm)

Title: Human genome analysis with long reads from nanopore sequencing