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Proceedings Paper

Comparison of bioinformatics programs for analysis of single nucleotide variants
Author(s): Agnieszka Skarzyńska; Magdalena Pawełkowicz; Wojciech Pląder
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Paper Abstract

Changes in genomic sequence might influence the gene expression, protein function and, what is related to phenotype of the organism. The Next Generation Sequencing provides a big amount of data that could be used in predicting the single nucleotide variants between analyzed and reference genome. Herein we compare three tools for predicting the structural variants: Freebayes, GATK toolkit and DeepVariant. Predictions with usage of each program were made on cucumber lines and the results were compared. Our analysis indicates that in order to obtain more precise and reliable variant predictions it is worth to use more than one program for detecting polymorphisms and cross-check the results.

Paper Details

Date Published: 1 October 2018
PDF: 9 pages
Proc. SPIE 10808, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2018, 1080834 (1 October 2018); doi: 10.1117/12.2501342
Show Author Affiliations
Agnieszka Skarzyńska, Warsaw Univ. of Life Sciences (Poland)
Magdalena Pawełkowicz, Warsaw Univ. of Life Sciences (Poland)
Wojciech Pląder, Warsaw Univ. of Life Sciences (Poland)


Published in SPIE Proceedings Vol. 10808:
Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2018
Ryszard S. Romaniuk; Maciej Linczuk, Editor(s)

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