arden-analyze - analyze the results of the artificial reference
genome mapping
arden-analyze [options] [INPUT FILE]
[OUTPUTFOLDER] ...
Script to analyze the results of the artificial reference genome
mapping. This script identifies the putative TPs / FPs on a specific data
set (reads).
- 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]