The software handles batches of trace data from sequencing instruments. It performs all processing except base calling (although it can employ third party programs such as phred for this step). This includes file format conversions, quality clipping, scanning for mutations and heterozygotes, multiple sequence alignment, easy visual inspection of traces, production of reports, and the accumulation and storage of readings and traces. The software also handles the initialisation/configuration of standard reference files and databases for any project. The two main programs are pregap4 and gap4. Pregap4 (see section Pregap4 introduction) prepares data for gap4 by automatically using a variety of smaller programs, including those used to search for mutations: tracediff (see section Trace Difference) and hetscan (see section Heterozygote Scanner). Gap4 (see section Gap4 introduction) is used to store the aligned readings, to view the sequences and traces, and to produce a report listing the observed mutations.
Any number of sequences can be processed in a single run, and for each individual patient sample the operation is generally performed in two steps. First, via pregap4, the traces are aligned and compared to the reference traces and any possible mutations or heterozygous bases marked. Secondly, the data is transfered into a gap4 database from where users can visually check the differences between the reference and patient traces.
The programs tracediff (see section Trace Difference) and hetscan (see section Heterozygote Scanner), can automatically compare patient and reference traces to find point mutations and heterozygous bases. Users can set parameters which control the sensistivity of the algorithms (and hence which determine the ratio of false negative and positive results). Tracediff adds tags of type "mutation" to the patient files, and hetscan of type "heterozygous". The tags contain the numerical scores achieved at the site of the reported base changes, and they can be viewed via the gap4 editor(see section Editing in gap4). Tracediff and hetscan are normally run via pregap4 (see section Pregap4 introduction).
The description of the programs given below is presented in reverse order of use i.e. gap4 then pregap4, but first we give further details about the use of reference data.