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 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