Partek Flow 4.0 is designed specifically for the analysis needs of next-generation sequencing applications including RNA, small RNA and DNA sequencing. With the ability to either build custom analysis pipelines or download pre-built pipelines, users can perform alignment, quantification, quality control, statistics and visualization. Using simple point-and-click actions, the software allows users to measure gene expression levels, discover coding SNPs, identify differential expression at the gene and transcript level, and detect gene fusions and novel isoforms. Statistical tests include multi-factor mixed model ANOVA test, a TPM normalization option, and Fisher’s exact test to find enriched gene sets and perform biological interpretation.