picopore 0.2.1

A tool for reducing the size of Oxford Nanopore Technologies' datasets without losing information.

# Picopore v 0.2.0 #

A tool for reducing the size of Oxford Nanopore Technologies' datasets without losing information.

Options:
- Lossless compression: reduces footprint without reducing the ability to use other nanopore tools by using HDF5's inbuilt gzip functionality
- Deep lossless compression: reduces footprint without removing any data by indexing basecalled dataset to the event detection dataset
- Raw compression: reduces footprint by removing event detection and basecall data, leaving only raw signal, configuration data and FASTQ
- Minimal compression: reduces footprint by removing event detection and basecall data, leaving only raw signal (not yet implemented)

## Installation ##

The latest stable version of Picopore is available on PyPi. Install it using ```pip install picopore```. For the bleeding edge, clone and install from GitHub.
```
git clone https://www.github.com/scottgigante/picopore
cd picopore
python setup.py install
```

### Requirements ###

Picopore requires ```h5repack``` from ```hdf5-tools```, which can be downloaded from https://support.hdfgroup.org/downloads/index.html or using ```sudo apt-get install hdf5-tools```.

Picopore requires the following Python packages:
* h5py

For live compression on a Nanopore run, it is recommended that you install ```npreader```.

## Usage ##

```
usage: picopore [-h] [-v] [-y] [--revert] [-t THREADS] [-g GROUP]
[--prefix PREFIX] [--test]
{lossless,deep-lossless,raw} [input [input ...]]
```

```
positional arguments:
{lossless,deep-lossless,raw}
choose compression mode (default: deep-lossless)
input list of directories or fast5 files to shrink

optional arguments:
-h, --help show this help message and exit
-v, --version show version number and exit
-y skip confirm step
--revert reverts files to original size (lossless modes only)
-t THREADS, --threads THREADS
number of threads (default: 1)
-g GROUP, --group GROUP
group number allows discrimination between different
basecalling runs (default: all)
--prefix PREFIX add prefix to output files to prevent overwrite
--test compress to a temporary file and check that all
datasets and attributes are equal (note: does not work
on pre-compressed files)
```

It is necessary to choose one compression mode out of ```lossless```, ```deep-lossless```, ```raw```, and ```minimal```.

Note that only ```lossless``` and ```deep-lossless``` are options for ```--revert``.

### Live Compression ###

To reduce the size of files during a MinION run, use npReader as follows:

```jsa.np.npreader -folder /path/to/reads -output - | picopore [options]```

You can download npReader at https://github.com/mdcao/npReader/

## Compression Modes ##

Picopore compression allows most nanopore tools to operate unimpeded. We provide a list of software tools which can operate on compressed files unimpeded, and the process required to recover the necessary data if this is not possible.

| Functionality | Lossless | Deep Lossless | Raw | Minimal |
|:--------------------:|:--------:|:-----------------------:|:---:|:-------:|
| Metrichor | ✓ | ```picopore --revert``` | ✓ | ✓ |
| nanonetcall | ✓ | ```picopore --revert``` | ✓ | ✓ |
| poretools fastq | ✓ | ```picopore --revert``` | ✓ | ```nanonetcall \ Metrichor``` |
| nanopolish consensus | ✓ | ```picopore --revert``` | ```nanonetcall \ Metrichor``` | ```nanonetcall \ Metrichor``` |


## FAQs ##

### Why would I want to shrink my fast5 files? ###

Nanopore runs are big. Really big. Over a long period of time, the storage footprint of a Nanopore lab will increase to unsustainable levels.

A large proportion of the data stored in ONT's fast5 files is unnecessary for the average end-user; during the basecalling process, a large amount of intermediary data is generated, and for most users who simply need the FASTQ, this data is useless.

Picopore solves this problem. Without removing the raw signal or configuration data used for basecalling, Picopore removes the intermediary datasets to reduce the size of your Nanopore dataset.

### Do I lose functionality when using Picopore? ###

Lossless compression uses HDF5's builtin compression, so all existing fast5 tools will work seamlessly.
- Use case: power users who wish to reduce server storage footprint

Deep lossless compression modifies the structure of your fast5 file: any data extraction tools will not work until you run ```python picopore.py --revert deep-lossless [input]```.
- Use case: power users who wish to reduce the size of their files during data transfer, or for long-term storage

Raw compression removes the "squiggle-space" data. For most users, this data is not critical; the only tools we know of which use the squiggle-space data are ```nanopolish```, ```nanoraw``` and ```nanonettrain```. If you do not intend on using these tools, your tools will work as before. If you do intend to use these tools, the raw signal is retained, and you can resubmit the files for basecalling to generate new squiggle-space data.
- Use case: end users who are only interested in using the FASTQ data
- Use case: power users running local basecalling with limited local disk space, who wish to use FASTQ immediately and will submit reads to Metrichor at a later date

Minimal compression removes all data not required to rerun basecalling on the fast5 files. This is only recommended for long-term storage, and requires files to be re-basecalled for any data to be retrieved.
- Use case: users storing historical runs for archive purposes, with no short-term plans to use these reads

### Do I lose any data when using Picopore? ###

Technically yes, but nothing that cannot be recovered. In the case where you need to access the data which has been removed, you can regenerate it using either picopore (on lossless compression) or using any basecaller provided by ONT (for other methods.)

Note that, since ONT's base calling is continuously improving, the basecalls generated when re-basecalling your data may not be the same, but in fact higher quality than before. If it is important that you retain the squiggle-space of the original called sequence, it is recommended that you use a lossless compression method.