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]