Alternative splicing (AS) and nonsense-mediated mRNA decay (NMD) are highly conserved cellular mechanisms that modulate gene expression. Here we introduce NMD pipeline that computes how splicing events introduce premature termination codons to mRNA transcripts via frameshift, then predicts the rate of PTC-dependent NMD. We utilize whole blood, deep RNA-sequencing data from critically ill patients to study gene expression in sepsis. Statistical significance was determined as adjusted p value < 0.05 and |log2foldchange| > 2 for differential gene expression and probability >= 0.9 and |DeltaPsi| > 0.1 for AS. NMD pipeline was developed based on AS data from Whippet. We demonstrate that the rate of NMD is higher in sepsis and deceased groups compared to control and survived groups, which signify purposeful downregulation of transcripts by AS-NMD or aberrant splicing due to altered physiology. Predominance of non-exon skipping events was associated with disease and mortality states. The NMD pipeline also revealed proteins with potential novel roles in sepsis. Together, these results emphasize the utility of NMD pipeline in studying AS-NMD along with differential gene expression and discovering potential protein targets in sepsis.