Rafael Ferreira da Silva

PGen: large-scale genomic variations analysis workflow and browser in SoyKB

TitlePGen: large-scale genomic variations analysis workflow and browser in SoyKB
Publication TypeJournal Article
Year of Publication2016
AuthorsY. Liu, S. M. Khan, J. Wang, M. Rynge, Y. Zhang, S. Zeng, S. Chen, J. V. Maldonado dos Santos, B. Valliyodan, P. P. Calyam, N. Merchant, H. T. Nguyen, D. Xu, and T. Joshi
JournalBMC Bioinformatics

With the advances in next-generation sequencing (NGS) technology and significant reductions in sequencing costs, it is now possible to sequence large collections of germplasm in crops for detecting genome-scale genetic variations and to apply the knowledge towards improvements in traits. To efficiently facilitate large-scale NGS resequencing data analysis of genomic variations, we have developed PGen, an integrated and optimized workflow using the Extreme Science and Engineering Discovery Environment (XSEDE) high-performance computing (HPC) virtual system, iPlant cloud data storage resources and Pegasus workflow management system (Pegasus-WMS). The workflow allows users to identify single nucleotide polymorphisms (SNPs) and insertion-deletions (indels), perform SNP annotations and conduct copy number variation analyses on multiple resequencing datasets in a user-friendly and seamless way.