Warning
These documents are not maintained and their instructions may be out of date. However the GED Lab does maintain the khmer protocols which may cover similar topics. See also the installation instructions for the current version of the khmer project.
Start up an m1.large.
Install screed:
cd /usr/local/share
git clone https://github.com/ged-lab/screed.git
cd screed
python setup.py install
Install khmer:
cd /usr/local/share
git clone https://github.com/ged-lab/khmer.git
cd khmer
make
Then, grab the following IPython Notebook:
cd /usr/local/notebooks
curl -O https://raw.github.com/ngs-docs/ngs-notebooks/master/ngs-5x-kmer-abundance-distributions-2013.ipynb
Now, go to your IPython Notebook interface (https:// + machine name) and open the notebok ‘ngs-5x-kmer-abundance-distributions-2013.ipynb’.