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’)
4.13.4. See also¶
jsa.np.npreader, jsa.util.streamServer, jsa.util.streamClient