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توضیحات

Large copy-number variation detector with low-depth whole-genome sequencing data

ویژگی	مقدار
سیستم عامل	-
نام فایل	cytocad-1.0.3
نام	cytocad
نسخه کتابخانه	1.0.3
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Tham Cheng Yong
ایمیل نویسنده	cytham@nus.edu.sg
آدرس صفحه اصلی	https://github.com/cytham/cytocad
آدرس اینترنتی	https://pypi.org/project/cytocad/
مجوز	gpl-3.0

## 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.

زبان مورد نیاز

مقدار	نام
>=3.6	Python

نحوه نصب

نصب پکیج whl cytocad-1.0.3:

pip install cytocad-1.0.3.whl

نصب پکیج tar.gz cytocad-1.0.3:

pip install cytocad-1.0.3.tar.gz