Count the median/avg k-mer abundance for each sequence in the input file, based on the k-mer counts in the given k-mer countgraph. Can be used to estimate expression levels (mRNAseq) or coverage (genomic/metagenomic). The output file contains sequence id, median, average, stddev, and seq length. For khmer 1.x count-median.py will split sequence names at the first space which means that some sequence formats (e.g. paired FASTQ in Casava 1.8 format) will yield uninformative names. Use --csv to fix this behavior.

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