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seen Aug 1 '14 at 5:16

comment Recommended sequence clustering algorithm for transcriptome data
Yeah, memory is going to be the limiting factor. I did just set up CD-Hit on my machine, so I'll give that a try.
comment Which way to run BLAST?
Thanks for your response. I'll be using the BLAST results to construct a "hints" file for use with the Augustus gene prediction program, so this isn't generating my final gene model. That said, it still might be better to use one of the programs you mention.