Computational Considerations in Transcriptome Assemblies and Their Evaluation, using High Quality Human RNA-Seq data
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It is crucial to understand the performance of transcriptome assemblies to improve current practices. Investigating the factors that affect a transcriptome assembly is very important and is the primary goal of our project. To that end, we designed a multi-step pipeline consisting of variety of pre-processing and quality control steps. XSEDE allocations enabled us to achieve the computational demands of the project. The high memory Blacklight and Greenfield systems at Pittsburgh Supercomputing Center were essential to accomplish multiple steps of this project. This paper presents the computational aspects of our comprehensive transcriptome assembly and validation study.
author list (cited authors)
Ghaffari, N., Abante, J., Singh, R., Blood, P. D., & Johnson, C. D.