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khmer: Normalize By Median (version 3.0.0a3+galaxy2)
Put in order of precedence such as longest reads first.
The tool will fail if given improperly paired reads and this option is selected.
By default this tool process reads in a pair-aware manner. This option disables that behavior.
If all but one of your sequence files are interleaved paired end reads you can include one unpaired file to be processed last without regard to pairing.
The inputs file(s) will be processed using the kmer counts in the specified k-mer countgraph file as a starting point.
ksize, n_tables, a specific tablesize

Do digital normalization (remove mostly redundant sequences)

Discard sequences based on whether or not their median k-mer abundance lies above a specified cutoff. Kept sequences will be placed in <fileN>.keep.

By default, Paired end reads will be considered together; if either read will be kept, then both will be kept. (This keeps both reads from a fragment, and helps with retention of repeats.) Unpaired reads are treated individually.

If --paired is set then proper pairing is required and the tool will exit on unpaired reads, although --unpaired-reads can be used to supply a file of orphan reads to be read after the paired reads.

--force_single will ignore all pairing information and treat reads individually.

With -s/--savegraph, the k-mer countgraph will be saved to the specified file after all sequences have been processed. --loadgraph will load the specified k-mer countgraph before processing the specified files. Note that the countgraph is in same format as those produced by load-into-counting.py and consumed by abundance-dist.py.

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