picopore-realtime1

Monitors a directory for new reads and compresses them in real time

Usage

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 ...]]

Overview

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)

Releases

Unchanged in 3 releases since Debian 11 (Bullseye).

11–13