Those Who Conducted the Study
- Nazlı S. Kara, İstinye University
- Meltem Kutnu, METU
- Yasemin Utkueri, Sabancı University
- Funda Yılmaz, Radbound University
- Elif Bozlak, University of Veterinary Medicine Vienna; Vienna Graduate School of Population Genetics
- Evrim Fer, University of Arizona
Abstract
The 2020 BioHackathon hosted the development of existing variant detection workflows for COVID-19 or the creation of new workflows to analyse the large amounts of data generated. Some of these include Galaxy Project, INSaFLU and nf-core. These workflows analyse genome data sequenced with next generation sequencing technology and output annotated single nucleotide polymorphism (SNP) and short insertion-deletion (indel) variants. They have different advantages and disadvantages according to the algorithms they use. In this study, we aimed to compare the SARS-CoV-2 genome variants published by the Galaxy Project with the variants identified by the INSaFLU workflow, so that we could evaluate the performance of these two workflows. As a result, we found nearly 600 variants common to both workflows. We found that almost half of these variants were in replicase polyprotein 1ab. We found that non-synonymous variants were more common than synonymous variants. The common and unique variants identified in this study can be analysed in more detail in future studies.
Date: June 21st, 2020 – 20:00 (GMT+3)
Language: Turkish
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