Plasmodium 3D7 Genome Assembly With PacBio Data and CLEAR

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