Metadata-Version: 1.1
Name: picopore
Version: 1.2.0
Summary: A tool for reducing the size of Oxford Nanopore Technologies' datasets without losing information.
Home-page: https://github.com/scottgigante/picopore
Author: Scott Gigante
Author-email: scottgigante@gmail.com
License: UNKNOWN
Description: Picopore v1.2.0
        ===============
        
        A tool for reducing the size of Oxford Nanopore Technologies' datasets without losing information.
        
        If you find Picopore useful, please cite it at http://dx.doi.org/10.12688/f1000research.11022.1
        
        Options:
        
        * Raw compression: reduces footprint by removing event detection and basecall data, leaving only raw signal, configuration data and a choice of FASTQ data, basecall summary, both or neither;
        * Lossless compression: reduces footprint without reducing the ability to use other nanopore tools by using HDF5's inbuilt gzip functionality; *(NOTE: as of May 2017, Oxford Nanopore Technologies implemented all compression strategies used in Picopore's lossless compression. Recently basecalled files will therefore not benefit from this compression.)*
        * Deep lossless compression: reduces footprint without removing any data by indexing basecalled dataset to the event detection dataset. *(NOTE: deep lossless compression will have the greatest impact on 2D datasets. Further work to implement 1D^2 compression is in progress.)*
        
        Author: Scott Gigante, Walter & Eliza Hall Institute of Medical
        Research. Contact: `Email <mailto:gigante.s@wehi.edu.au>`_, `Twitter <http://www.twitter.com/scottgigante>`_
        
        Installation
        ------------
        
        Install via pypi
        ~~~~~~~~~~~~~~~~
        
        The latest stable version of Picopore is available on PyPi. Install it using the following command:
        
        ::
        
            pip install picopore
        
        Install via conda
        ~~~~~~~~~~~~~~~~~
        
        Picopore and dependencies could also be installed using conda.
        
        ::
        
            conda install picopore -c bioconda -c conda-forge
        
        Install from source
        ~~~~~~~~~~~~~~~~~~~
        
        For the bleeding edge, clone and install from GitHub.
        
        ::
        
            git clone https://www.github.com/scottgigante/picopore
            cd picopore
            python setup.py install
        
        Currently, ``h5py`` is only available on Windows via ``conda``.
        
        Requirements
        ~~~~~~~~~~~~
        
        Picopore runs on Python 2.7, 3.4, 3.5, 3.6 or 3.7 with development headers (``python-dev`` or similar).
        
        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`` or similar.
        
        Picopore requires the following Python packages:
        
        * ``h5py``
        * ``future``
        * ``watchdog`` (for real-time compression)
        
        In addition, ``h5py`` requires HDF5 1.8.4 or later (``libhdf5-dev`` or similar). Difficulties resolving dependencies of ``h5py`` can be resolved by installing from your package manager, using ``sudo apt-get install python-h5py`` or similar.
        
        Usage
        -----
        
        ::
        
            commands: picopore
                      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
        
        ::
        
            usage: 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 ...]]
        
        ::
        
            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: --no-
                                    summary)
              --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)
        
        It is necessary to choose one compression mode out of ``lossless``,
        ``deep-lossless``, and ``raw``.
        
        Note that only ``lossless`` and ``deep-lossless`` are options for ``--revert``.
        
        For ``--manual`` raw compression, the entire group path is used for matching. For example,
        you could use the command ``picopore --mode raw --manual 1D.*Events [...]`` to remove the
        groups ``/Analyses/Basecall_1D_000/BaseCalled_template/Events`` and
        ``/Analyses/Basecall_1D_000/BaseCalled_complement/Events``.
        
        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                           Raw ``--no-fastq``
        ====================== ============= ======================= ============================= =============================
        Metrichor               yes           ``picopore --revert``   yes                          yes
        nanonetcall             yes           ``picopore --revert``   yes                          yes
        poretools fastq         yes           ``picopore --revert``   yes                          ``nanonetcall / Metrichor``
        poRe printfastq         yes           ``picopore --revert``   yes                          ``nanonetcall / Metrichor``
        nanopolish consensus    yes           ``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
        ^^^^^^^^
        
        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
        ^^^^^^^^^^^^^
        
        Deep lossless compression modifies the structure of your fast5 file: any
        data extraction tools will not work until you run
        ``python picopore.py --revert --mode 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
        ^^^
        
        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
        
        Raw ``--no-fastq``
        ^^^^^^^^^^^^^^^^^^
        
        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.
        
Keywords: nanopore,compression,hdf5,fast5,oxford,minion
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
