---
name: "picopore"
section: "1"
platform: "linux"
package: "picopore"
version: "1.2.0-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/picopore"
---

# picopore(1)

reducing the size of an Oxford Nanopore Technologies dataset without losing any data

## NAME

picopore - reducing the size of an Oxford Nanopore Technologies dataset without losing any data

## SYNOPSIS

**picopore** \[-h\] **--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

## OPTIONS

### See also:

- picopore-realtime

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

- picopore-test

  compresses to temporary files and checks that all datasets and attributes are equal (lossless modes only)

- picopore-rename

  renames groups and datasets within FAST5 files

### 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.