Tregwiki:Assembling promotors from trace databases
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Apart from a complete assembly, which might be more feasible than I thought before (see our discussion on nodalpoint) you can try the following tools:
- Genotrace (paper) is a service that does exactly that - it assembles your sequence from traces using SSAHA and phrap. You can download it and install it on your own machine. Installing has a couple of requirements (Llinux, BioPerl, SSAHA, dust, phrap/crossmatch). If your cannot find the right traces on the website you might also simply ask the author if he can't add your favorite organism.
- the article about the phusion assemlber gives a good overview of various assemblers...