So, I recently gave SOAPdenovo2 a try on a large genome assembly which I'd previously been using Velvet and Ray on. I know SOAP was used with great success on te Giant Panda among many others. One setting of question for me right now is the global "maximal read length". I have a number of both PE and MP sets from HiSeq that are 101bp long. But, I also have a set of PE from MiSeq that is 267bp long. It would seem that you would do as instructed and assign max_rd_len to be the 267 number, but does that have an adverse affect on all of the 101bp stuff?
#maximal read length
max_rd_len=267
Couldn't find an example where you set this within the [LIB] parameters for each individual set of data...
#maximal read length
max_rd_len=267
Couldn't find an example where you set this within the [LIB] parameters for each individual set of data...
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