CATFISHQ(1)

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.