Hi Andrea,
We are using reliable and effective SNP/InDel search algorithm
without taking into consideration trace files.
Our custom pipeline to find SNP/InDel candidates is written in Python.
Detailed instructions and source code are available at:
http://cgpdb.ucdavis.edu/SNP_Discovery/
Then we visualize and validate candidates using Python Contig Viewer:
http://cgpdb.ucdavis.edu/SNP_Discovery/Py_ContigViewer/
Contig Viewer provides semiautomatic oligo design for PCR.
Feedback and comments are very welcome.
Alexander Kozik,
Department of Vegetable Crops,
University of California, Davis
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