Metadata-Version: 2.1
Name: runHiC
Version: 0.8.5
Summary: A easy-to-use Hi-C processing software supporting distributed computation
Home-page: https://github.com/XiaoTaoWang/HiC_pipeline
Author: XiaoTao Wang
Author-email: wangxiaotao686@gmail.com
License: UNKNOWN
Description: runHiC
        ******
        .. image:: https://zenodo.org/badge/doi/10.5281/zenodo.55324.svg
           :target: http://dx.doi.org/10.5281/zenodo.55324
        .. image:: https://static.pepy.tech/personalized-badge/runhic?period=total&units=international_system&left_color=black&right_color=orange&left_text=Downloads
           :target: https://pepy.tech/project/runhic
        
        runHiC is an easy-to-use command-line tool for Hi-C data processing.
        
        Since versio 0.8.5, runHiC has changed the default aligner to `chromap <https://github.com/haowenz/chromap>`_,
        which is comparable to `bwa-mem <https://github.com/lh3/bwa>`_ in alignment accuracy, but runs over 10 times faster.
        
        Since version 0.8.1, runHiC can be used directly on `Arima HiC <https://arimagenomics.com>`_ data
        by setting the enzyme name to *Arima*.
        
        Since version 0.8.0, runHiC has changed its default data container/format from HDF5 to
        `Pairs <https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md>`_ and
        `Cooler <https://github.com/mirnylab/cooler>`_. 
        
        Design Concepts
        ===============
        runHiC is designed to process Hi-C data from raw sequencing reads(.sra, .fastq, .fastq.gz) to the ICE-corrected
        contact matrices. It currently contains 5 subcommand:
        
        +------------+-------------------------------------------------------------------------------------------------------------------+
        | mapping    | Map raw pair-end sequencing data to a supplied genome. Support three read aligners: chromap, bwa and minimap2.    |
        +------------+-------------------------------------------------------------------------------------------------------------------+
        | filtering  | Perform read-level and fragment-level noise removing                                                              |
        +------------+-------------------------------------------------------------------------------------------------------------------+
        | binning    | 1.Generate contact matirx; 2. Perform ICE/matrix-balancing normalization                                          |
        +------------+-------------------------------------------------------------------------------------------------------------------+
        | pileup     | Perform entire processing from *mapping* to *binning*                                                             |
        +------------+-------------------------------------------------------------------------------------------------------------------+
        | quality    | Assess the quality of your Hi-C data                                                                              |
        +------------+-------------------------------------------------------------------------------------------------------------------+
        
        Links
        =====
        - `Detailed Documentation <http://xiaotaowang.github.io/HiC_pipeline/>`_
            - `Installation <http://xiaotaowang.github.io/HiC_pipeline/install.html>`_
            - `Quick Start <http://xiaotaowang.github.io/HiC_pipeline/quickstart.html>`_
            - `Data Quality <http://xiaotaowang.github.io/HiC_pipeline/quality.html>`_
            - `Parallel Computation <http://xiaotaowang.github.io/HiC_pipeline/parallel.html>`_
        - `Code Repository <https://github.com/XiaoTaoWang/HiC_pipeline/>`_ (At GitHub, Track the package issue)
        - `PyPI <https://pypi.python.org/pypi/runHiC>`_ (Download and Installation)
        
        Usage
        =====
        Open a terminal, type ``runHiC -h`` or ``runHiC <subcommand> -h`` for help information.
        
        Citation
        ========
        Xiaotao Wang. (2016). runHiC: A user-friendly Hi-C data processing software based on hiclib. Zenodo.
        `10.5281/zenodo.55324 <http://dx.doi.org/10.5281/zenodo.55324>`_
        
Keywords: Hi-C Arima ICE cooler pairs bioinformatics pipeline
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Operating System :: POSIX
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/x-rst
