NAME
picopore-realtime - monitors a directory for new reads and compresses them in real time
SYNOPSIS
picopore-realtime [-h] --mode {lossless,deep-lossless,raw} [--revert] [--fastq] [--summary] [--manual STR] [-v] [-y] [-t INT] [--prefix STR] [--skip-root] [--print-every INT] [input [input ...]]
DESCRIPTION
A tool for reducing the size of an Oxford Nanopore Technologies dataset without losing any data
picopore-realtime monitors a directory for new reads and compresses them in real time
OPTIONS
positional arguments:
- input
-
list of directories or fast5 files to shrink
optional arguments:
- -h, --help
-
show this help message and exit
- --mode {lossless,deep-lossless,raw}
-
choose compression mode
- --revert
-
reverts files to original size (lossless modes only)
- --fastq, --no-fastq
-
retain FASTQ data (raw mode only) (Default: --fastq)
- --summary, --no-summary
-
retain summary data (raw mode only) (Default: --nosummary)
- --manual STR
-
manually remove only groups whose paths contain STR (raw mode only, regular expressions permitted, overrides defaults)
- -v, --version
-
show version number and exit
- -y
-
skip confirm step
- -t INT, --threads INT
-
number of threads (Default: 1)
- --prefix STR
-
add prefix to output files to prevent overwrite
- --skip-root, --no-skip-root
-
ignore files in root input directories for albacore realtime compression (Default: --no-skip-root)
- --print-every INT
-
print a dot every approximately INT files, or -1 to silence (Default: 100)
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.