Overview of the re-sequencing data analysis process integrated with the pipeline. An example of the entire process of re-sequencing analysis for a specific genomic region from a set of individuals. (A) Re-sequencing steps, base calling, alignment and heterozygous site identification for an entire region sharing a reference sequence. (B) PolyPhred output files of discontinuous sub-regions, such as exons, re-sequenced independently. (C) Consolidation of different exons of a gene that were independently amplified and re-sequenced using the same reference genomic sequence. (D) Files formats that can be handled by the pipeline either as input or output files.