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.. _tutorial:
NanoOK tutorial
===============
#. Follow the installation instructions to install NanoOK on your
system. Docker and a VM are also options.
#. Download the `example E. coli
dataset <http://opendata.earlham.ac.uk/nanook/nanook_ecoli_500.tar.gz>`__
from http://opendata.earlham.ac.uk/nanook/ and uncompress::
tar -xvf nanook_ecoli_500.tar.gz
#. Change into the directory::
cd nanook_ecoli_500
#. Index the reference with LAST::
cd references
lastdb -Q 0 ecoli_dh10b_cs ecoli_dh10b_cs.fasta
cd ..
#. Extract FASTA::
nanook extract -s N79596_dh10b_8kb_11022015
#. Perform alignments::
nanook align -s N79596_dh10b_8kb_11022015 -r references/ecoli_dh10b_cs.fasta
#. Generate a report::
nanook analyse -s N79596_dh10b_8kb_11022015 -r references/ecoli_dh10b_cs.fasta -passonly
#. View the PDF file inside ``N79596_dh10b_8kb_11022015/latex``
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