GO-056

2021-02-22

2022-02-22

Primary data analysis for next generation sequencing result, conversion and quality control of raw reads to .VCF files

dr Agnieszka Golińska

Next Generation Sequencing (NGS) is considered the most advanced and comprehensive method of genotyping for biological samples. Different type of platforms as well as targeted sequencing for specific gene panels, whole exome sequencing (WES), whole genome sequencing (WGS), and long read sequencing technologies are available for implementation of genome sequencing in every aspect of research and studies. While the methods are also adopted by many clinical centers for patient genomic data handling, the raw data analysis and subsequent interpretation of result for such tests and methods are still considered a cumbersome bioinformatics task for many people, including the academic investigators. It has been recommended that a primary knowledge in Linux/Linux based systems (Ubuntu) and programming languages as well as Python and R is necessary for NGS data analysis. The aim of this study is the establishment and set up an updated pipeline for preprocessing next generation DNA sequencing data through advanced and available computational facilities in UWB. The result of this investigation could be used in other studies which applied NGS technologies for DNA sequencing. In collaboration with Medical University of Bialystok (MUB), a sample of raw sequencing data also obtained from the ongoing Pharmacogenomics project by the investigators of department of analysis and bioanalysis of medicines.