Metadata-Version: 1.0
Name: chanjo
Version: 0.3.0
Summary: A coverage analysis package for clinical sequencing.
Home-page: http://chanjo.readthedocs.org/
Author: Robin Andeer
Author-email: robin.andeer@gmail.com
License: MIT
Download-URL: https://github.com/robinandeer/chanjo
Description: .. image:: https://raw.github.com/robinandeer/chanjo2/develop/assets/chanjo-banner.png
          :alt: Chanjo banner
        
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        .. image:: https://travis-ci.org/robinandeer/chanjo.png?branch=develop
          :target: https://travis-ci.org/robinandeer/chanjo
          :alt: Build Status
        
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          :alt: Bitdeli Badge
        
        *Chanjo* (Swahili, lit. *vaccine*) is a sane coverage analysis tool focusing on clinical sequencing. It aims to simplify answering clinically relevant questions like: *how well is my gene of interest covered?*.
        
        .. code-block:: console
        
          $ chanjo annotate db.sqlite using test.bam EGFR ALB CD4 BRCA1 --sample "fancy_sample_id"
          $ chanjo peak db.sqlite EGFR
          {
              "EGFR": [
                  {
                      "sample": "fancy_sample_id",
                      "completeness": 1.0,
                      "coverage": 227.64
                  }
              ]
          }
        
        Are you more interested in the Python API? Check out the official documentation_.
        
        Introduction
        --------------
        Verifying adequate read coverage is an `important task`_ to ensure robustness in clinical sequencing. Enabling this in collaboration with clinicians demand new software developed with physicians rather than researchers in mind.
        
        `Alternative tools`_ often hide intuitive genetic concepts such as genes, transcripts, and exons behind more fundamental, less descriptive abstractions. When it comes to the most well defined `genetic elements`_, this can be likened to requiring knowledge of programming to use a computer.
        
        *Chanjo* reads coverage directly from a BAM alignment making it a good fit in most bioinformatic pipelines. A portable yet powerful SQLite database consolidates the output. The ambitions is to create a `standardized API`_ for coverage across the exome.
        
        Completeness (NEW)
        ~~~~~~~~~~~~~~~~~~~
        The *completeness* metric is one concrete new feature you will get for free using Chanjo. It's meant as a complement to average coverage as a measure of the success of coverage.
        
        Completeness works as such. Decide on a cutoff "X" representing the lower limit of adequate coverage (e.g. 10x reads). Completeness is simply the percentage of bases across an element/interval that with coverage >= X.
        
        I believe completeness to be a more useful assessment of coverage success than average coverage for at least many clinical purposes.
        
        Contribute
        -----------
        Test and submit issues. Learn more and point out shortcomings in the extended documentation_. For more details I'll try to keep issues and milestones up-to-date as a source of what needs to be worked on.
        
        Contributors
        -------------
        Robin Andeer
        
        License
        --------
        MIT
        
        .. _documentation: https://chanjo.readthedocs.org/en/latest/
        
        .. _important task: http://www.pnas.org/content/106/45/19096.abstract
        
        .. _Alternative tools: http://bedtools.readthedocs.org/en/latest/
        
        .. _genetic elements: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2704439/
        
        .. _standardized API: http://gemini.readthedocs.org/en/latest/
Keywords: coverage sequencing clinical exome
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
