A Software Environment for DNA Sequencing

 

We have continued the development of a prototype software environment in support of DNA sequencing called "FAKtory". The environment consists of (1) Gene Myers' software library, FAK II, for the core combinatorial problem of assembling fragments, (2) a Tcl/Tk based interface, and (3) a software suite supporting a database of fragments and a processing pipeline that includes clipping, tagging, and vector removal modules. A key feature of FAKtory is that it is highly customizable: the structure of the fragment database, the processing pipeline, and the operation of each phase of the pipeline are specifiable by the user. Yet such customization need only be established once at a given site, subsequently users see a relatively simple system tailored to their needs.

 

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