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

ARDEN-ANALYZE(1) User Commands ARDEN-ANALYZE(1)

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]
February 2014 arden-analyze 2013-04-25