Development of a Genomic Analysis Pipeline for Use on DoD High-Performance Computing Resources

Author(s):

Margaret M. Hurley

Abstract:

Increased use of next-generation sequencing in research has led to a concomitant growth in available software to analyze this data. We rely heavily on high-performance computing resources for this work and discuss suitable software options in each step of the analysis pipeline. Multiple options are provided for each step to take advantage of strengths of the algorithms for the disparate use cases (e.g., prokaryotic vs. eukaryotic organisms) studied during the project. We pay particular attention to the genomic assembly algorithms and the heart of the pipeline and provide a detailed comparison between assembly results from our sample sets.