By default, phred is not bundled with staden package. However, I can use it to do base calling for raw trace file. It appeared that staden package can also provide phred-like quality score (quality accuracy estimation). Does the staden io_lib do base calling? Or, it just read the base calling result from trace files? How about the quality score? I am writting a web-based trace processing pipeline, since phred is not open-source, I am considering using staden io_lib to do base calling and create phred-like quality score. Does this sound crazy? Any suggestion is highly appreciated!
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