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With the booming of next generation sequencing technology and itsimplementation in clinical practice and life science research, the need forfaster and more efficient data analysis methods becomes pressing in the fieldof sequencing. Here we report on the evaluation of an optimized germlinemutation calling pipeline, HummingBird, by assessing its performance againstthe widely accepted BWA-GATK pipeline. We found that the HummingBird pipelinecan significantly reduce the running time of the primary data analysis forwhole genome sequencing and whole exome sequencing while without significantlysacrificing the variant calling accuracy. Thus, we conclude that expansion ofsuch software usage will help to improve the primary data analysis efficiencyfor next generation sequencing.

Computational Performance of a Germline Variant Calling Pipeline for Next Generation Sequencing