Single Base Variant Calling Based on Reference Genome and Reads

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Ghareghani, Maryam | 2016

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Type of Document: M.Sc. Thesis
Language: Farsi
Document No: 48292 (02)
University: Sharif University of Technology
Department: Mathematical Sciences
Advisor(s): Khazaei, Shahram; Motahari, Abolfazl
Abstract:
Genome sequencing is one of the fundamental problems in today’s Biology. It has applications in significant problems such as finding association between an individual’s genome sequence and his phenotypes, discovering new genes, and finding evolutionary relations between organisms. Following the rapid advances in sequencing technologies and generation of a huge amount of short reads, efficient computational tools are needed for processing sequencing data. Shortness of reads is a factor that makes the task of reconstructing repetitive genomic regions complicated. In fact, the main challenge in both sequencing and resequencing problems is reconstruction of repeat regions. Common resequencing tools usually use simple local algorithms for variant calling and have low precision in redundant genomic regions. Considering the complexity arising from repeat structures in genome, we have designed a novel algorithm for resequencing that has high accuracy in calling repeat regions
Keywords:
Resequencing ; Sequencing ; Read ; Repeat Regions ; Variant Calling