table of contents
| CATFISHQ(1) | User Commands | 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.
| May 2021 | catfishq 1.1.3+ds |