A few examples

See the examples directory for complete examples.

STAMPS data set

The 'stamps' data set is a fake metagenome-like data set containing two species, mixed at a 10:1 ratio. The source genomes are in data/stamps-genomes.fa. The reads file is in data/stamps-reads.fa.gz, and consists of 100-base reads with a 1% error rate.

The example shows how to construct k-mer abundance histograms, as well as the effect of digital normalization and partitioning on the k-mer abundance distribution.

See the script for running everything and the IPython Notebook.

For an overall discussion and some slides to explain what's going on, visit the Web site for a 2013 HMP metagenome assembly webinar that Titus Brown gave.

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