Plasmodium 3D7 Genome Assembly With PacBio Data and CLEAR

<p>This fileset contains data, code and IPython Notebooks demostrating<br>how to assemble the hard to assemble 80% AT-rich Plasmodium 3D7 genome.</p> <p>The first thing you might want to do is probably to read through<br>''P3D7_CLEAR_NOTE.pdf'' to know what this dataset is about.</p> <p>You will have to "gunzip" the two main data file ''preads.fa.gz'' and<br>''pr_pr_strigent.m4.gz'' to use them.</p> <p>The IPython Notebook ''P3D7_CLEAR_NOTE.ipynb'' and ''P3D7_CLEAR_NOTE_P2.ipynb''<br>can be run to generate the assembly if you have proper computation environment.</p> <p>There are also the PDF verison of the notebooks, ''P3D7_CLEAR_NOTE.pdf''<br>and ''P3D7_CLEAR_NOTE_P2.pdf''. Some requirement on how to reproduce the<br>computational experiment can be found in ''P3D7_CLEAR_NOTE.pdf''.</p> <p>Thanks Carsten Russ (Broad Institute) and Sarah Volkmann (Harvard School of Public Health) for providing the DNA sample.