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khmer: Filter reads (version 3.0.0a3+galaxy2)
Put in order of precedence such as longest reads first.
Only trim when a sequence has high enough coverage; median abundance > 20
Trim at k-mers below this abundance
The abundances of the k-mers in the input nucleotide sequence file will be calculated using the kmer counts in this k-mer countgraph.

Trims fastq/fasta sequences at k-mers of a given abundance based on a provided k-mer countgraph

If the input sequences are from RNAseq or metagenome sequencing then --variable-coverage should be used.

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