Metadata-Version: 2.1
Name: cytocad
Version: 1.0.3
Summary: Large copy-number variation detector with low-depth whole-genome sequencing data
Home-page: https://github.com/cytham/cytocad
Author: Tham Cheng Yong
Author-email: cytham@nus.edu.sg
License: gpl-3.0
Download-URL: https://github.com/cytham/cytocad/releases
Description: 
        ## CytoCAD - Copy-number variation caller using low-depth whole-genome sequencing data
        [![Build Status](https://app.travis-ci.com/cytham/cytocad.svg?branch=master)](https://app.travis-ci.com/github/cytham/cytocad)
        [![PyPI pyversions](https://img.shields.io/pypi/pyversions/cytocad)](https://pypi.org/project/cytocad/)
        [![PyPI versions](https://img.shields.io/pypi/v/cytocad)](https://pypi.org/project/cytocad/)
        [![Conda](https://img.shields.io/conda/v/bioconda/cytocad)](https://anaconda.org/bioconda/cytocad)
        [![Github release](https://img.shields.io/github/v/release/cytham/cytocad?include_prereleases)](../../releases)
        [![PyPI license](https://img.shields.io/pypi/l/cytocad)](./LICENSE.txt)
        
        <p align="center">
          <img src="https://user-images.githubusercontent.com/25361260/131828572-bfb57cf8-e9e2-4f8d-b200-5b4b5a5b8181.png" width="500" alt="accessibility text" align='center'>
        </p>
        
        CytoCAD is a bioinformatics tool for the identification of large genomic copy-number variation through coverage anomaly detection
         (CAD) using mapped whole-genome sequencing (WGS) data. It has been tested in low-depth (~8X) Oxford Nanopore WGS long-read
          data. Its output displays chromosome illustrations demarcating regions of copy-number gains (Red) or losses (Blue). The above illustration shows a loss of one chromosome 7 copy, a gain of one chromosome 21 copy, a partial duplication of both chromosome 8 copies, and a loss of one chromosome 17 short arm. It also has two X chromosomes and no Y chromosome, suggesting a female sex.
        
        ### Basic information:
        * Takes as input a mapped whole-genome sequencing BAM file and output a BED file and a chromosome ideogram-like figure
        * Uses [Ruptures](https://github.com/deepcharles/ruptures) python package for change point detection of read coverage data per
         chromosome 
        * Uses [tagore](https://github.com/jordanlab/tagore) for chromosome ideogram illustrations
        
        ## Getting Started
        
        ### Quick run
        
        ```
        cytocad [Options] sample.bam working_dir 
        ```
        
        | Argument | Comment |
        | :--- | :--- |
        | sample.bam | Input mapped WGS BAM file |
        | working_dir | Working directory |
        
        #### Output
        | Output file | Comment |
        | :--- | :--- |
        | ${sample}.ideo.svg | Chromosome ideogram produced by [tagore](https://github.com/jordanlab/tagore) |
        | ${sample}.CNV.bed | BED file of chromosome regions with CNV |
        
        For more information, see [wiki](https://github.com/cytham/cytocad/wiki).
        
        ### Operating system: 
        * Linux (x86_64 architecture, tested in Ubuntu 16.04)  
        
        ### Installation:
        There are three ways to install CytoCAD:
        #### Option 1: Conda (Recommended)
        ```
        # Installing from bioconda automatically installs all dependencies 
        conda install -c bioconda cytocad
        ```
        #### Option 2: PyPI (See dependencies below)
        ```
        # Installing from PyPI requires own installation of dependencies, see below
        pip install cytocad
        ```
        #### Option 3: GitHub (See dependencies below)
        ```
        # Installing from GitHub requires own installation of dependencies, see below
        git clone https://github.com/cytham/cytocad.git 
        cd cytocad
        pip install .
        ```
        
        ### Installation of dependencies
        * bedtools >=2.26.0
        * samtools >=1.3.0
        * rsvg-convert >=2.40.13
        
        Please make sure each executable binary is in PATH.
        ##### 1. _bedtools_
        Please visit [here](https://bedtools.readthedocs.io/en/latest/content/installation.html) for instructions to install.
        
        ##### 2. _samtools_
        Please visit [here](http://www.htslib.org/download/) for instructions to install.
        
        ##### 3. _rsvg-convert_
        ```
        sudo apt-get update
        sudo apt-get install librsvg2-bin
        ```
        
        ## Versioning
        See [CHANGELOG](./CHANGELOG.txt)
        
        ## Citation
        
        Not available yet
        
        ## Author
        
        * **Tham Cheng Yong** - [cytham](https://github.com/cytham)
        
        ## License
        
        This project is licensed under GNU General Public License - see [LICENSE.txt](./LICENSE.txt) for details.
        
        ## Limitations
        * Chromosome pairs illustrated by tagore may resemble sister chromatids, but they are in fact homologous pairs
        * Phasing of CNVs for each chromosome homologous pair is not yet possible.
        * The default minimum size of detectable CNV is about 500 kb. It can be adjusted by the 'interval' and 'rolling' parameters
         following the equation: minimum size ~= interval*rolling 
        * Other chromosomal structural variations, such as inversions, have to be detected by other tools, such as [NanoVar](https://github.com/cytham/nanovar). NanoVar has incorporated CytoCAD in its pipeline from version 1.4.0 onwards.
        
Keywords: cytocad,copy number variation,CNV,whole genome sequencing,low depth,change point detection
Platform: UNKNOWN
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/markdown
