NanoOK

NanoOK

# installation & prerequites
$ sudo apt-get update
$ sudo apt-get install last r-base r-cran-ggplot2 hdf5-tools \
  texlive texlive-latex-extra default-jre git

# Insert following two lines in .profile
export NANOOK_DIR=/path/to/NanoOK
export PATH=/path/to/NanoOK/bin:$PATH

$ source .profile
# to check the installation
$ nanook                     

# To run NanoOK, 'fast5' dir containing PASS/FAIL dir's is required.
$ mkdir fast5
$ mv PASS FAIL fast5

# For genome indexing, go to the dir with genome.fa
$ lastdb -Q 0 genome genome.fa

# FASTA extraction (-s = sample dir which is containing 'fast5' dir)
$ nanook extract -s .

# Alignment
$ nanook align -s . -r genome.fa

# Analysis
$ nanook analyse -s . -r genome.fa -passonly