Overview of the VIP pipeline. Overview of the Variant Identification Pipeline (black arrows and white text-boxes) and the VIP Validator (grey arrows and grey text-boxes). The analysis pipeline consists of 4 modules. 1) Raw sequences are extracted from the FASTA files generated by the GS-FLX sequencer and processed into sequenced amplicons and additional information. 2a) Reference amplicons are generated using a list of reference sequences and the list of primers. 2b) Mapping is carried out with BLAT using the reference amplicons and the sequenced amplicons. Variations are detected and stored in the database. 3) The requested reports are generated. The VIP Validator introduces additional variation in the sequence reads and reanalyses those sequences to validate the pipeline for that specific variation.