4.13. jsa.np.filter: Filter sequencing data

jsa.np.filter filters sequencing data based on sequence read type, length and quality. Examples of its usage can be found on jsa.np.npreader.

4.13.1. Synopsis

jsa.np.filter: Filter nanopore reads data from fastq file

4.13.2. Usage

jsa.np.filter [options]

4.13.3. Options

--input=s Name of the input file, - for standard input (REQUIRED)
--output=s Name of the output file, - for standard output (REQUIRED)
--lenMin=i Minimum sequence length (default=‘0’)
--lenMax=i Minimum sequence length (default=‘2147483647’)
--qualMin=d Minimum average quality (default=‘0.0’)
--qualMax=d Maximum average quality (default=‘1000.0’)
--group=s Group need to be extracted, leave blank for selecting all groups (default=’‘)
--excl2D Exclude 2D reads (default=’false’)
--exclTemp Exclude template reads (default=’false’)
--exclComp Exclude complement reads (default=’false’)
--format=s Format of the output file (default=’fastq’)
--help Display this usage and exit (default=’false’)