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arden-filter - Online in the Cloud

Run arden-filter in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command arden-filter that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


arden-filter - filter a SAM file based on the analysis with ARDEN

SYNOPSIS


arden-filter [INPUT SAM] [OUTPUTFILE] [OPTIONS]...

DESCRIPTION


Script to filter and a SAM file based on the analysis with ARDEN. It is necessary to
specify the desired cutoffs for RQS,GAPS and MM. Type: python filter -e 1 for printing
some examples.

OPTIONS


Required Arguments:

OUTPUTFILE
Outputfilename

INPUT Single SAM file to filter.

--version
show program's version number and exit

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

-r RQS, --rqs=RQS
Threshold for minimum read quality score.. [default: 0]

-m MM, --mismatches=MM
Threshold for maximum number of mismatches in an alignment [default: 3]

-g GAPS, --gaps=GAPS
Threshold for maximum number of gaps in an alignment. [default: 3]

-e PEXAMPLES, --examples=PEXAMPLES
set to 1 if you want to print examples

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