NAME

       catfishq - concatenates fastq files

DESCRIPTION

       usage: catfishq [-h]

              [--log  {DEBUG,INFO,WARNING,ERROR,CRITICAL,debug,info,warning,error,critical}]  [-o
              OUT]   [-l   MIN_LEN]   [-q   MIN_QSCORE]   [--max-sequencing-time    MAX_SEQ_TIME]
              [--min-sequencing-time MIN_SEQ_TIME] [--start-time START_TIME] [--print-start-time]
              [-n MAX_N] [-b MAX_BP] [-r] [-d] FASTQ [FASTQ ...]

       Cat long lists of FASTQ files

   positional arguments:
       FASTQ  FASTQ files or folders containing FASTQ files

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

       --log {DEBUG,INFO,WARNING,ERROR,CRITICAL,debug,info,warning,error,critical}
              Print debug information

       -o OUT, --output OUT
              Output file. (default: stdout)

       -l MIN_LEN, --min-length MIN_LEN
              Minimum read length

       -q MIN_QSCORE, --min-qscore MIN_QSCORE
              Minimum q-score

       --max-sequencing-time MAX_SEQ_TIME
              Only output reads that where sequenced up to the given time (minutes).

       --min-sequencing-time MIN_SEQ_TIME
              Only output reads that where sequenced after the given time (minutes).

       --start-time START_TIME
              Starttime of the run as guppy time stamp (only required with --sequencing-time). If
              'min' is given as argument the minimal time is detected automatically.

       --print-start-time
              Print the minimal start_time of all fastq files

       -n MAX_N, --max_n MAX_N
              Stop after <max_n> reads

       -b MAX_BP, --max_mbp MAX_BP
              Stop after <max_bp> mega base pairs

       -r, --recursive
              Search folders recursively

       -d, --dedup
              Remove duplicated reads.

AUTHOR

        This manpage was written by Steffen Moeller for the Debian distribution and
        can be used for any other usage of the program.