*De novo* genome assembly
=======================

A module in the fall 2015 edition of INF-BIOx121

Slides:

- Introduction to the assembly module `pptx <https://github.com/lexnederbragt/INF-BIOx121/raw/2015/Assembly/presentations/01_intro_to_assembly_module.pptx>`__
- Principles and problems of *de novo* genome assembly `pptx <https://github.com/lexnederbragt/INF-BIOx121/raw/2015/Assembly/presentations/02_Principles_and_problems_of_de_novo_genome_assembly.pptx>`__
- Assembly before and after `pptx <https://github.com/lexnederbragt/INF-BIOx121/raw/2015/Assembly/presentations/03_Assembly_before_and_after.pptx>`__


Practicals:

.. toctree::
   :maxdepth: 1

   README
   practicals/02_Assembly_using_velvet
   practicals/03_Mapping_reads_to_an_assembly
   practicals/04_Assembly_improvement_using_REAPR
   practicals/05_Assembly_using_HGAP
   practicals/06_Assembly_using_SPADES
   practicals/07_Comparing_assemblies_to_the_reference
   practicals/Sources

Content of the `etherpad <https://github.com/lexnederbragt/INF-BIOx121/blob/2015/Assembly/etherpad.txt>`__