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Old 01-22-2015, 12:00 PM   #5
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Well... fastx has some disadvantages in terms of speed and lack of support for paired files, not to mention the fact that it uses a sub-par trimming algorithm. You might try BBDuk, which runs on Mac without needing recompilation, does quality-trimming or filtering much faster than fastx, and supports paired reads.
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