rodenluo/mixcr

MiXCR is a universal software for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data.

This is a Chinese translation of the documentation of MiXCR.

这是 MiXCR 说明文档的中文翻译。

The copyright of MiXCR belongs to Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail. See Liscense for more detail.

MiXCR 的版权归 Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail，详见 使用许可

Overview 概述

MiXCR is a universal software for fast and accurate analysis of raw T- or B- cell receptor repertoire sequencing data. MiXCR是一个通用软件，用以快速并准确地分析 T细胞 和 B细胞 受体库测序的原始数据。

Installation / Download 安装 / 下载

Using Homebrew on Mac OS X or Linux (linuxbrew)

使用 Mac OS X 里的 Homebrew 或 Linux 的 linuxbrew

brew install milaboratory/all/mixcr

to upgrade already installed MiXCR to the newest version:

升级已安装的MiXCR到最新版本：

brew update
brew upgrade mixcr

Manual install (any OS) 手动安装（任何操作系统）

• download latest MiXCR version from release page
• 从 发行页 下载最新版的MiXCR
• unzip the archive
• 解压缩压缩包
• add resulting folder to your PATH variable
• 添加解压缩后的文件夹到你的环境变量 PATH 中
  • or add symbolic link for mixcr script to your bin folder
  • 或者为 mixcr脚本 添加快捷方式到你的 bin 文件夹
  • or use MiXCR directly by specifying full path to the executable script
  • 或者通过指定到可执行脚本的全部路径来使用 MiXCR

Requirements 要求

• Any OS with Java support (Linux, Windows, Mac OS X, etc..)
• 任何支持 Java 的操作系统 (Linux, Windows, Mac OS X, 等)
• Java 1.8 or higher
• Jave 1.8 或更高版本

Usage 用法

Here is a very simple example of analysis of raw human RepSeq data:

这是一个非常简单的例子，分析人的RepSeq原始数据的：

mixcr align -r log.txt input_R1.fastq.gz input_R2.fastq.gz alignments.vdjca
mixcr assemble -r log.txt alignments.vdjca clones.clns
mixcr exportClones clones.clns clones.txt

this sequence of commands will produce a tab-delimited list of clones (clones.txt) assembled by their CDR3 sequences with extensive information on their abondancies, V, D and J genes etc.

这一串命令将会生成一个制表符分割的克隆的列表 (clones.txt)， 这是通过他们 CDR3 的序列来组装的，以及大量的关于他们的丰度，V，D，J 基因等。

For more details see documentation.

更多细节，请见说明文档。

Documentation 说明文档

Detailed documentation can be found at https://mixcr.readthedocs.io/

详细的说明文档在 https://mixcr.readthedocs.io/ 详细的中文说明文档在 https://mixcr-cn.readthedocs.io/

License 使用许可

Copyright (c) 2014-2015, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail (here and after addressed as Inventors) All Rights Reserved

Copyright (c) 2014-2015, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail （这里及以下，作为发明人发表） 保留所有权利。

Permission to use, copy, modify and distribute any part of this program for educational, research and non-profit purposes, by non-profit institutions only, without fee, and without a written agreement is hereby granted, provided that the above copyright notice, this paragraph and the following three paragraphs appear in all copies.

特此授予许可，仅限非盈利机构因教育、研究、和非盈利目的而使用、复制、修改、和发布该软件任一部分， 不需付费，也不需取得书面协议。

Those desiring to incorporate this work into commercial products or use for commercial purposes should contact the Inventors using one of the following email addresses: [email protected], [email protected]

想要将这项工作纳入商业产品中或是因商业目的使用它，应该使用下列Email地址中的一个联系 发明人：[email protected], [email protected]

IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY PATENT, TRADEMARK OR OTHER RIGHTS.

Cite 引用

Bolotin, Dmitriy A., Stanislav Poslavsky, Igor Mitrophanov, Mikhail Shugay, Ilgar Z. Mamedov, Ekaterina V. Putintseva, and Dmitriy M. Chudakov. "MiXCR: software for comprehensive adaptive immunity profiling." Nature methods 12, no. 5 (2015): 380-381.

Files referenced in original paper 原文献中引用的文件

Can be found here.

可以在这里找到。