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

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

nanook 1.26                                      September 2017                                        NANOOK(1)

        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.

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

extractoptions:-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

   alignoptions:-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

   analyseoptions:-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

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

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

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

   processoptions:-process <file> specifies a process file

   Readtypeoptions:-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

   Otheroptions:-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

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