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Evaluation of post denovo assembly next generation sequencing data

Master thesis - Supervised by Prof. Dr. Dmitrij Frishman ( & Dr. Nicolas Straube

As part of the project “Hering Lachs und Karpfen- alte Bekannte mit unbekannter Verwandtschaft“ financed by the Volkswagenstiftung, we aim to reconstruct a molecular phylogeny of “basal” Clupeocephalan fishes.

The generated data is based on a gene capture approach targeting 14,000 putative ortholog exons and subsequent next-generation sequencing. The Master candidate is supposed to analyze the influence of different denovo assembly methods and settings, to collect knowledge on suitable settings for maximizing the information extracted from millions of Next-Generation-Sequencing-reads.

Post assembly analyses comparing the captured and assembled sequence information to the reference (the zebrafish Danio rerio) are further useful to evaluate the efficiency of the assembly tools available.


 Aim of the study:

  • Optimized assembly settings for denovo assembly of reads.
  • Conduction of parallized tests of k-mer values using the denovo assembler ABySS.
  • Evaluation of assembly success using the Perl script bingene (Li et al 2013*).
  • Documentation of an analysis pipeline for finding optimized settings for denovo assembly.


*Li C, Hofreiter M, Straube N, Corrigan S, Naylor GJP: Capturing protein-coding genes across highly divergent species. Biotechniques 2013, 54: 321-326, doi:10.2144/000114039.



Prof. Dmitrij Frishman, Fachgebiet Bioinformatik, Wissenschaftszentrum Weihenstephan,