See the ‘examples’ subdirectory for complete examples.
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.
This file can be edited directly through the Web. Anyone can update and fix errors in this document with few clicks -- no downloads needed.
For an introduction to the documentation format please see the reST primer.