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Evaluation of Base Calling Methods in Next Generation Sequencing

Gharibi, Hadi | 2015

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 47413 (05)
  4. University: Sharif University of Technology
  5. Department: Electrical Engineering
  6. Advisor(s): Hossein Khalaj, Babak; Motahhari, Abolfazl
  7. Abstract:
  8. In the mid twentieth century by discovering the existence of genetic strands and understanding their role in diseases and phenotypes of species, research initiated to decipher their content. Sequencing of the first human genome at early twenty-first century paved the way to study and even cure complex human deseases having genetic origin. Next Generation Sequencing (NGS) Technologies have significantly reduced the expenses and the timing complexity of DNA Sequencing and this has an improving trend. In this thesis, we evaluate Base Calling methods, a critical step in analyzing next generation sequencing information and deals with massive sequencing data. Base Calling tries to optimally detect the elements of the genome or the bases (A, G, C, and T) from the raw output data of the sequencing platform. In other words, Base-Calling produces reads for reconstructing the target genome by processing the Illumina platform intensity data. First off, we study error factors in NGS base calling methods, compare their performance in terms of accuracy and run speed, and also represent new methods to reduce base calling error. Afterwards, base calling error propagation is studied and required base calling accuracy is determined for resequencing. Variant calling error consisting of false positives and false negatives are calculated and it is shown that the base calling error can be tolerated until a certain threshold and above that the error increases dramatically. At last, the effect of the repeat regions on the genome are explored utilizing bacterial and random genomes
  9. Keywords:
  10. Next Generation Networks ; Mapping Algorithm ; DNA ; Base Calling ; Read ; Resequencing ; Variant

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