Sep 15

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9th CCoE Seminar: “A case study in bioinformatics software engineering: SeqAn”

reinert_pic_2013On Thursday, Oct. 9, 2013, at 3 p.m. (at TU Dresden, Willersbau Room A317) Prof. Dr. Knut Reinert from FU Berlin will present his work in the field of using GPUs for bioinformatics.


In this talk I will convey to you my view about the necessary steps for enabling efficient research in biomedical research in the times where biotechnology can give us comprehensive views of certain data. I will start by arguing that the NGS technologies developed in the recent years changed the research landscape to a degree similar to the beginning of the millennium when the human genome was initially sequenced.  As a consequence, the research tools of many biomedical researcher have or will change in the sense that they will conductlarge scale, complex computations. Hence, as a community, we have to turn our focus to how we develop such tools.

Thinking about this becomes essential since in the near future clinical decisions concerning the treatment of individuals (personalised medicine) will be based on such computations. I will then talk how many of these goals can be reached by using software libraries and exemplify that on the SeqAn library developed in my lab. SeqAn (www.seqan.de) is an open-source C++ template library (BSD license) that implements many efficient and generic data structures and algorithms for Next-Generation Sequencing (NGS) analysis. It contains gapped k-mer indices, enhanced suffix arrays (ESA) or an FM-index, as well algorithms for fast and accurate alignment or read mapping. Based on those data types and fast I/O routines, users can easily develop tools that are extremely efficient and easy to maintain. I will talk about the design of SeqAn and how it allows to integrate other tools as well as to support hardware acceleration (Multicore and GPGPU).

Permanent link to this article: https://gcoe-dresden.de/8th-ccoe-seminar-a-case-study-in-bioinformatics-software-engineering-seqan/