NAME

       arden-analyze - analyze the results of the artificial reference genome mapping

SYNOPSIS

       arden-analyze [options] [INPUT FILE] [OUTPUTFOLDER] ...

DESCRIPTION

       Script  to  analyze  the  results  of the artificial reference genome mapping. This script identifies the
       putative TPs / FPs on a specific data set (reads).

OPTIONS

       OUTPUTFOLDER
              path to output destination folder.

       INPUT FILE
              ppath to ini file. To get the required format have a look at the example files.

       --version
              show program's version number and exit

       -h, --help
              show this help message and exit

       -p PHRED, --phred=PHRED
              Specify the PHRED encoding of the input reads i.e.  Illumina 1.3+ = -p 33.[default: 33]

       -r RANK, --internalrank=RANK
              Use internal ranking for reads (needed if the read names cannot be lexicographically be sorted  in
              the same way in python and your OS by sam tools).[default:1]