Comparison of Galaxy and Unix tools for analyzing the exome sequencing data from syndactyly abnormalities

Nguyen Thy Ngoc; Huynh Minh Huong

doi:10.15625/2525-2518/20054

Author affiliations

Authors

Nguyen Thy Ngoc University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Nghia Do Ward, Ha Noi, Viet Nam https://orcid.org/0000-0002-3181-9209
Huynh Minh Huong University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Nghia Do Ward, Ha Noi, Viet Nam

DOI:

https://doi.org/10.15625/2525-2518/20054

Keywords:

GALAXY, exome sequencing, high performance computing, syndactyly, pipeline

Abstract

Syndactyly is a common congenital limb malformation characterized by the fusion of digits resulting from incomplete separation during embryonic development. Advances in exome sequencing have enabled the identification of genetic variants associated with congenital disorders, while bioinformatics platforms play a crucial role in data analysis and interpretation. This study compared exome sequencing data from a 1.5-year-old syndactyly patient analyzed using two bioinformatics platforms, GALAXY and UNIX. Using the GRCh38/hg38 reference genome, UNIX identified 275,572 variants, whereas GALAXY detected 140,291 variants. Comparative analysis revealed 126,848 shared variants between the two platforms. Filtering against a panel of 200 syndactyly-associated genes reduced the dataset to 1,345 variants distributed across the genome, with notable concentrations on chromosomes 2, 4, and 11. Among the analyzed genes, FRAS1, CACNA1C, GLI2, and NOTCH1 exhibited the highest variant frequencies. The findings demonstrate that the choice of bioinformatics platform significantly influences variant detection outcomes. GALAXY offers accessibility and reproducibility, whereas UNIX provides greater flexibility and computational performance, supporting optimized exome sequencing workflows for genetic studies of congenital limb abnormalities.

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