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khmer: Extract partitions (version 3.0.0a3+galaxy2)
Put in order of precedence such as longest reads first.
No more than this many number of sequences will be stored in each output
The minimum partition size worth keeping (--min-partition-size/-m)
(--output-unassigned/-U)

Separate sequences that are annotated with partitions into grouped files.

(from the khmer project: http://khmer.readthedocs.org/en/v2.0/ )