catfishq - concatenates fastq files
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
- FASTQ
- FASTQ files or folders containing FASTQ files
- -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.
This manpage was written by Steffen Moeller for the Debian
distribution and
can be used for any other usage of the program.