Phineus and Staden

The Staden tracefile processing system (http://staden.sourceforge.net/) is a highly effective and widely used solution for handling the processing of tracefiles for large projects, where the user wishes to create and edit contigs composed of overlapping sequences.
Unfortunately, because it is not designed for small projects, such as thos examining several loci, using sequences derived from PCR products with variable primers and (usually) only 2 sequences (forward and reverse) for each 'contig', it provides a less than optimal solution for MLST-type projects.

Staden does however include a number of modules which carry out the various processing steps required in both large scale genomic projects and small scale multiple loci MLST-like projects. Therefore, Phineus, like STARS, makes use of these modules to perform the required processing on ABI format chromatograms to give the 'finished' sequence for use in MLST-like projects.

Phineus also includes the capability for users to create and use their own modules providing a scaleable and expandable system.

A fundamental difference between the STARS workflow and the Phineus workflow is the inclusion of a clipping module written specifically for use with MLST/MLSA sequences and discussed on the next page.

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