catfishq1

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.