.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH PICOPORE-REALTIME "1" "June 2020" "picopore-realtime 1.2.0" "User Commands"
.SH NAME
picopore-realtime \- monitors a directory for new reads and compresses them in real time
.SH SYNOPSIS
.B picopore\-realtime
[\-h] \fB\-\-mode\fR {lossless,deep\-lossless,raw} [\-\-revert]
[\-\-fastq] [\-\-summary] [\-\-manual STR] [\-v] [\-y]
[\-t INT] [\-\-prefix STR] [\-\-skip\-root]
[\-\-print\-every INT]
[input [input ...]]
.SH DESCRIPTION
A tool for reducing the size of an Oxford Nanopore Technologies dataset without losing any data
.PP
picopore\-realtime monitors a directory for new reads and compresses them in real time
.SH OPTIONS
.SS "positional arguments:"
.TP
input
list of directories or fast5 files to shrink
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-mode\fR {lossless,deep\-lossless,raw}
choose compression mode
.TP
\fB\-\-revert\fR
reverts files to original size (lossless modes only)
.TP
\fB\-\-fastq\fR, \fB\-\-no\-fastq\fR
retain FASTQ data (raw mode only) (Default: \fB\-\-fastq\fR)
.TP
\fB\-\-summary\fR, \fB\-\-no\-summary\fR
retain summary data (raw mode only) (Default: \fB\-\-nosummary\fR)
.TP
\fB\-\-manual\fR STR
manually remove only groups whose paths contain STR
(raw mode only, regular expressions permitted,
overrides defaults)
.TP
\fB\-v\fR, \fB\-\-version\fR
show version number and exit
.TP
\fB\-y\fR
skip confirm step
.TP
\fB\-t\fR INT, \fB\-\-threads\fR INT
number of threads (Default: 1)
.TP
\fB\-\-prefix\fR STR
add prefix to output files to prevent overwrite
.TP
\fB\-\-skip\-root\fR, \fB\-\-no\-skip\-root\fR
ignore files in root input directories for albacore
realtime compression (Default: \fB\-\-no\-skip\-root\fR)
.TP
\fB\-\-print\-every\fR INT
print a dot every approximately INT files, or \fB\-1\fR to
silence (Default: 100)
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.