GINGER is a tool that is implemented an integrated method for gene structure prediction in higher eukaryotes. RNA-Seq-based methods, ab initio-based methods, homology-based methods are performed, and then gene structures are reconstructed via dynamic programming with appropriately weighted and scored exon/intron/intergenic regions. Different prediction processes and filtering criteria are applied to multi-exon and single-exon genes. This pipeline is implemented using Nextflow.