Modification of the short read alignment algorithm to improve the quality of the human whole genome sequencing data processing pipeline
https://doi.org/10.15514/ISPRAS-2023-35(2)-17
Abstract
This study emphasizes the importance of aligning short reads in the analysis of human whole-genome sequencing data. The alignment process involves determining the positions of short genetic sequences relative to a known reference genome sequence of the human genome. Traditional alignment methods use a linear reference sequence, but this can lead to incorrect alignment, especially when short reads contain genetic variations. In this work, the index file of the reference sequence was modified using the minimap2 tool. Experimental results showed that adding information about frequently occurring genetic variations to the minimap2 index increases the number of correctly identified genetic variants, which affects the quality of subsequent data analysis.
About the Authors
Egor Pavlovich GUGUCHKIN
Institute for System Programming of the Russian Academy of Sciences
Russian Federation
Russian Federation
Egor Pavlovich GUGUCHKIN is a research fellow at ISP RAS. His research interests include the analysis of genetic data and the development of bioinformatics pipelines.
Evgeny Andreevich KARPULEVICH
Institute for System Programming of the Russian Academy of Sciences
Russian Federation
Russian Federation
Evgeny Andreevich KARPULEVICH is a specialist of the Information Systems Department. Research interests: application of data analysis algorithms to the biomedical domain, development of systems for distributed data storage and analysis.
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Review
For citations:
GUGUCHKIN E.P., KARPULEVICH E.A. Modification of the short read alignment algorithm to improve the quality of the human whole genome sequencing data processing pipeline. Proceedings of the Institute for System Programming of the RAS (Proceedings of ISP RAS). 2023;35(2):235-248. (In Russ.) https://doi.org/10.15514/ISPRAS-2023-35(2)-17
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