Ms@New - It works with MAQ 0.6.8; the source is not available; but I can send you the executable. CloudMAQ is a wrapper around MAQ and we have not modified the original MAQ; hence the results of CloudMAQ will be no different from MAQ.
BTW CloudMAQ works for 125bp Illumina reads too!!!
BTW CloudMAQ works for 125bp Illumina reads too!!!
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