.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.48.1.
.TH CATFISHQ "1" "May 2021" "catfishq 1.1.3+ds" "User Commands"
.SH NAME
catfishq \- concatenates fastq files
.SH DESCRIPTION
usage: catfishq [\-h]
.IP
[\-\-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 ...]
.PP
Cat long lists of FASTQ files
.SS "positional arguments:"
.TP
FASTQ
FASTQ files or folders containing FASTQ files
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-log\fR {DEBUG,INFO,WARNING,ERROR,CRITICAL,debug,info,warning,error,critical}
Print debug information
.TP
\fB\-o\fR OUT, \fB\-\-output\fR OUT
Output file. (default: stdout)
.TP
\fB\-l\fR MIN_LEN, \fB\-\-min\-length\fR MIN_LEN
Minimum read length
.TP
\fB\-q\fR MIN_QSCORE, \fB\-\-min\-qscore\fR MIN_QSCORE
Minimum q\-score
.TP
\fB\-\-max\-sequencing\-time\fR MAX_SEQ_TIME
Only output reads that where sequenced up to the given
time (minutes).
.TP
\fB\-\-min\-sequencing\-time\fR MIN_SEQ_TIME
Only output reads that where sequenced after the given
time (minutes).
.TP
\fB\-\-start\-time\fR START_TIME
Starttime of the run as guppy time stamp (only
required with \fB\-\-sequencing\-time\fR). If 'min' is given as
argument the minimal time is detected automatically.
.TP
\fB\-\-print\-start\-time\fR
Print the minimal start_time of all fastq files
.TP
\fB\-n\fR MAX_N, \fB\-\-max_n\fR MAX_N
Stop after <max_n> reads
.TP
\fB\-b\fR MAX_BP, \fB\-\-max_mbp\fR MAX_BP
Stop after <max_bp> mega base pairs
.TP
\fB\-r\fR, \fB\-\-recursive\fR
Search folders recursively
.TP
\fB\-d\fR, \fB\-\-dedup\fR
Remove duplicated reads.
.SH AUTHOR
 This manpage was written by Steffen Moeller for the Debian distribution and
 can be used for any other usage of the program.