Metadata-Version: 1.1
Name: covest
Version: 0.2.0
Summary: Covest estimates the coverage and genom size, just from k-mer abundance histogram computed from DNA sequences reads.
Home-page: https://github.com/mhozza/covest
Author: Michal Hozza
Author-email: mhozza@gmail.com
License: GNU GPLv3
Description: covest
        ======
        
        Tool that estimates coverage (and genome size) of dna sequence from
        reads.
        
        .. image:: https://badge.fury.io/py/covest.svg
            :target: https://badge.fury.io/py/covest 
        .. image:: https://travis-ci.org/mhozza/covest.svg?branch=master
            :target: https://travis-ci.org/mhozza/covest
        
        Installation
        ------------
        
        ``pip install covest``
        
        For development:
        ~~~~~~~~~~~~~~~~
        
        ``pip install -e .`` from the project directory
        
        Usage
        -----
        
        type ``covest --help`` for the usage.
        
        Other included tools
        --------------------
        
        -  ``geset.py`` tool for estimation genome size from reads and known
           coverage
        -  ``prepare_experient.py`` tool for experiment pipeline setup
        -  ``experiment_table.py`` tool which collects data from experiment and
           create a nice table (html, tex, and csv formats are supported)
        -  Read simulator:
        
           -  ``generate_sequence.py`` random sequence generator
           -  ``read_simulator.py`` tool for generating random reads form the
              sequence
        
        Copyright and citation
        ----------------------
        
        Covest is licenced under `GNU
        GPLv3 <http://www.gnu.org/licenses/gpl-3.0.en.html>`__ license.
        
        Covest is research software, so you should cite us when you use it in scientific publications!
           Hozza, M., Vinař, T., & Brejová, B. (2015, September). How Big is that Genome? Estimating Genome Size and Coverage from k-mer Abundance Spectra. In String Processing and Information Retrieval (pp. 199-209). Springer International Publishing.
        
Keywords: covest
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
