ssadedin/ximmer
ssadedin
自动构建
Ximmer: a system for running and evaluating CNV callers on exome and targeted genomic sequencing
1 次收藏下载次数: 0状态：自动构建维护者：ssadedin仓库类型：镜像最近更新：7 年前
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Ximmer
Ximmer is a tool designed to help users of exome and targeted genomic sequencing data accurately detect and interpret copy number variants (CNVs). Ximmer is not a copy number detection tool itself. Rather, it is a framework for running other copy number detection tools and interpreting their results. It offers three essential features that users of CNV detection tools need:
- A suite of pipelines for running a variety of well known CNV detection tools
- A simulation tool that can create artificial CNVs in sequencing data for the purpose of evaluating performance
- A visualisation and curation tool that can com***e results from multiple CNV detection tools and allow the user to inspect them, along with relevant annotations.
All of these are integrated into one streamlined package that you can run easily on any data set you want to analyse.
We created Ximmer because although there are very many CNV detection tools, they can be hard to run and their performance can be highly variable and hard to estimate. This is why Ximmer builds in simulation: to allow a quick and easy estimation of the performance of any tool on any data set.
See an online example report to get an idea what Ximmer's output looks like.
Requirements
- Java 1.7+
- Python 2.7, preferably the Anaconda installation (you will need support for pandas, numpy and other computational libraries that are not always easy to compile in a vanilla installation).
- R 3.2 or higher
- 24GB of RAM
or
- Use https://ssadedin.github.io/ximmer/docker.html!
Building and Running It
See the online https://ssadedin.github.io/ximmer/ for more details!
镜像拉取方式
您可以使用以下命令拉取该镜像。请将 <标签> 替换为具体的标签版本。如需查看所有可用标签版本，请访问 标签列表页面。
DockerHub 原生拉取命令
docker pull ssadedin/ximmer:<标签>
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oldzhang
运维工程师
Linux服务器
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"Docker访问体验非常流畅，大镜像也能快速完成下载。"