Master Degree / Yüksek Lisans Tezleri

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Author: search.filters.author.Bağcı, CanerSubject: search.filters.subject.Bioinformatics

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  • Master Thesis
    Automatic, Fast and Accurate Sequence Decontamination
    (Izmir Institute of Technology, 2016) Bağcı, Caner; Allmer, Jens; Tekir, Selma
    The introduction of massively parallel sequencing technologies was a revolutionary step in genomics. Their decreasing cost and powerful features have put them more and more on demand in the last decade. It is now possible to sequence even complete genomes of organisms, using massively parallel sequencing technologies even for small laboratories around the world. However, the power of this powerful technology comes with its challenges. The challenges are both in technological and computational side of the work. In this work, one of these computational challenges is addressed and a novel algorithm is offered to solve the problem. Sequencing by synthesis is one of the methods used in many different massively parallel sequencing instruments. This method utilizes the biological process of DNA replication and with the help of different means of detection, it allows sequencing a DNA molecule while it is replicated. Since DNA polymerase requires a primer to start the replication reaction, short oligonucleotide adapters are used in sequencing by synthesis methods to initiate the reaction. However, certain circumstances allow these adapters to contaminate final sequence reads. Several tools have been offered to trim adapters from reads; but all depend on the prior knowledge of the adapter sequence by the bioinformatician. In this work, an algorithm is offered to detect and trim adapters only using the sequences of reads, without relying on prior knowledge of adapter sequences. The algorithm was shown to perform better or on the same grounds with existing methods in terms of speed and efficiency.