NAME

       nanook  -  flexible,  multi-reference  software  for  pre-  and post-alignment analysis of
       nanopore sequencing data, quality and error profiles

SYNOPSIS

       nanook <extract|align|analyse|compare|process> [options]

DESCRIPTION

        NanoOK (pronounced na-nook) is a tool for extraction, alignment and
        analysis of Nanopore reads. NanoOK will extract reads as FASTA or FASTQ
        files, align them (with a choice of alignment tools), then generate a
        comprehensive multi-page PDF report containing yield, accuracy and
        quality analysis. Along the way, it generates plain text files which can
        be used for further analysis, as well as graphs suitable for inclusion
        in presentations and papers.

OPTIONS

   extract options:
       -s|-sample <dir> specifies sample directory

       -f|-reads specifies alternative dir for FAST5 files (default fast5)

              Can be  absolute  (beginning  with  /)  or  relative  e.g.  -f  reads/downloads  if
              replicating Metrichor file structure

       -a|-fasta specifies FASTA file extraction (default)

       -q|-fastq specifies FASTQ file extraction

       -basecallindex specifies the index of the analysis (default: latest)

       -mergereads to generate merged FASTA files in addition to single read files

       -minquality <value> to set the minimum quality for a 'pass' read

   align options:
       -s|-sample <dir> specifies sample directory

       -r|-reference <path> specifies path to reference database

       -aligner <name> specifies the aligner (default last)

       -alignerparams <params> specifies parameters to the aligner

       -showaligns echoes aligner commands to screen

   analyse options:
       -s|-sample <dir> specifies sample directory

       -r|-reference <path> specifies path to reference database

       -aligner <name> specifies the aligner (default last)

       -coveragebin <int> specifies coverage bin size (default 100)

       -bitmaps to output bitmap PNG graphs instead of PDF

   compare options:
       -l|-samplelist <file> specifies a sample list file

       -o|-outputdir <directory> specifies an output directory

       -type <2d|template|complement> specifies an output directory

   process options:
       -process <file> specifies a process file

   Read type options:
       -passonly to analyse only pass reads

       -failonly to analyse only fail reads

       -2donly to analyse only 2D reads

       -templateonly to analyse just Template reads

       -complementonly to analyse just Complement reads

   Other options:
       -t|-numthreads <number> specifies the number of threads to use (default 1)

       -log <filename> enables debug logging to file

       -force to force NanoOK to ignore warnings

       -timeout to set the number of seconds before giving up waiting for new reads (default 2)

       Valid aligners: last, bwa, blasr, marginalign, graphmap

AUTHOR

       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.