fastaq-filter

FASTAQ-FILTER(1)                 User Commands                FASTAQ-FILTER(1)



NAME
       fastaq_filter - Filter sequences to get a subset of them

DESCRIPTION
       usage: fastaq_filter [options] <infile> <outfile>

       Filters a sequence file by sequence length and/or by name matching a
       regular expression

   positional arguments:
       infile Name of input file to be filtered

       outfile
              Name of output file

   optional arguments:
       -h, --help
              show this help message and exit

       --min_length INT
              Minimum length of sequence to keep [0]

       --max_length INT
              Maximum length of sequence to keep [inf]

       --regex REGEX
              If given, only reads with a name matching the regular expression
              will be kept

       --ids_file FILENAME
              If given, only reads whose ID is in th given file will be used.
              One ID per line of file.

       -v, --invert
              Only keep sequences that do not match the filters

   Mate file for read pairs options:
       --mate_in FILENAME
              Name of mates input file. If used, must also provide --mate_out

       --mate_out FILENAME
              Name of mates output file

       --both_mates_pass
              By default, if either mate passes filter, then both reads
              output. Use this flag to require that both reads of a pair pass
              the filter



fastaq 3.17.0                      July 2018                  FASTAQ-FILTER(1)