  With the booming of next generation sequencing technology and its
implementation in clinical practice and life science research, the need for
faster and more efficient data analysis methods becomes pressing in the field
of sequencing. Here we report on the evaluation of an optimized germline
mutation calling pipeline, HummingBird, by assessing its performance against
the widely accepted BWA-GATK pipeline. We found that the HummingBird pipeline
can significantly reduce the running time of the primary data analysis for
whole genome sequencing and whole exome sequencing while without significantly
sacrificing the variant calling accuracy. Thus, we conclude that expansion of
such software usage will help to improve the primary data analysis efficiency
for next generation sequencing.
