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.. labibi documentation master file, created by
sphinx-quickstart on Sun Nov 4 10:10:29 2012.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
2013 CEMI Workshop at Caltech
=============================
=============== =============================================================
Day Schedule
=============== =============================================================
Tuesday 9/17 * 1:15pm: Igor Antoschechkin on local sequencing core
* 2pm Lecture: `Cloud computing etc. <_static/cemi-cloud-computing.pptx.pdf>`__
* Afternoon lab 1: :doc:`amazon/index`
* 3:30pm lecture: `BLAST <_static/cemi-lecture-blast.pptx.pdf>`__
* Afternoon lab 2: :doc:`tuesday`
* Final lecture: `A belated welcome! <_static/cemi-lecture-welcome.pptx.pdf>`__
Wednesday 9/18 * 9am: lecture, `Short read mapping <_static/cemi-lecture-mapping.pptx.pdf>`__
* morning lab: :doc:`reads_and_qc`
* morning lab 2: :doc:`bwa_mapping`
* 1:15pm: assembly exercise
* 2pm: lecture, `Assembly <_static/cemi-assembly.pptx.pdf>`__
Thursday 9/19 * lab: :doc:`assembly-lab` and :doc:`blastkit`
* ~10am: lecture: `metagenome assembly <_static/2013-cemi-metag-assembly.pptx.pdf>`__
* late morning lab: :doc:`prokka-annotation`
* afternoon lab: :doc:`some-exercises`
* afternoon lecture: `pipelines <_static/lecture5-pipelines.pdf>`__ and automation
* tutorial: `the shell <https://github.com/swcarpentry/boot-camps/tree/2013-06-wise-beginners/shell>`__
Friday 9/20 * **Arms building first floor (Buwalda Room 151A)**
* 9am: lecture: `metagenome assembly <_static/2013-cemi-assembly-methods.pptx.pdf>`__
* morning: open lab time to work through pipelines (see especially `Kalamazoo Metagenome Assembly <https://khmer-protocols.readthedocs.org/en/latest/metagenomics/>`__ and :doc:`some-exercises`
* :doc:`more-resources`
* Assembly :doc:`scavenger-hunt`
* **ends** 1pm; lunch with Titus, Chris, Yoshiki at Sansai.
=============== =============================================================
For even more resources on these topics, check out the course website for the
`GED's ANGUS course <http://ged.msu.edu/angus/>`__ which is run at MSU every summer.
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`