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Journal of Medical Signals and Sensors، جلد ۱۱، شماره ۱، صفحات ۳۷-۴۴
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عنوان انگلیسی Selection of Optimal Bioinformatic Tools and Proper Reference for Reducing the Alignment Error in Targeted Sequencing Data
چکیده انگلیسی مقاله Background: Careful design in the primary steps of a next-generation sequencing study is critical for obtaining successful results in downstream analysis. Subjects and Methods: In this study, a framework is proposed to evaluate and improve the sequence mapping in targeted regions of the reference genome. In this regard, simulated short reads were produced from the coding regions of the human genome and mapped to a Customized Target-Based Reference (CTBR) by the alignment tools that have been introduced recently. The short reads produced by different sequencing technologies aligned to the standard genome and also CTBR with and without well-defined mutation types where the amount of unmapped and misaligned reads and runtime was measured for comparison. Results: The results showed that the mapping accuracy of the reads generated from Illumina Hiseq2500 using Stampy as the alignment tool whenever the CTBR was used as reference was significantly better than other evaluated pipelines. Using CTBR for alignment significantly decreased the mapping error in comparison to other expanded or more limited references. While intentional mutations were imported in the reads, Stampy showed the minimum error of 1.67% using CTBR. However, the lowest error obtained by stampy too using whole genome and one chromosome as references was 3.78% and 20%, respectively. Maximum and minimum misalignment errors were observed on chromosome Y and 20, respectively. Conclusion: Therefore using the proposed framework in a clinical targeted sequencing study may lead to predict the error and improve the performance of variant calling regarding the genomic regions targeted in a clinical study.
کلیدواژه‌های انگلیسی مقاله Chromosomes, high-throughput nucleotide sequencing, sequence analysis
نویسندگان مقاله | Hannane Mohammadi Nodehi
Department of Medical Genetics, School of Medicine, Isfahan University of Medical Sciences Department of Bioinformatics, School of Advanced Technologies in Medicine, GenTArget Corp. (GTAC), Deputy of Research and Technology, Isfahan University of Medica Sciences, Isfahan, Iran


| Mohammad Amin Tabatabaiefar
Department of Bioelectric and Biomedical Engineering, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences


| Mohammadreza Sehhati


نشانی اینترنتی http://jmss.mui.ac.ir/index.php/jmss/article/view/564
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زبان مقاله منتشر شده en
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نوع مقاله منتشر شده Original Articles
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