diff --git a/README.md b/README.md index fd1d205..704429f 100644 --- a/README.md +++ b/README.md @@ -2,9 +2,9 @@ 本书是简单介绍病原微生物，特别是病原细菌的高通量测序数据分析。针对的用户主要是拥有自己的台式测序仪（比如 [Illumina][] [MiSeq][]）想分析自己数据结果，或者是希望能从高通量数据中获取更多信息的从事病原细菌的研究人员。如果阅读者有一定 [Linux][] 基础，会更好的理解本书中的一些示例。 -本书代码库位于 http://github.com/indexofire/bac-ngs-book.git ，作为测序领域的初学者，书中内容肯定会有许多错误之，非常欢迎大家提交 issues 或者 fork 代码库。 +本书代码可以从[这里](http://github.com/indexofire/bac-ngs-book.git)获得，本文内容肯定会有许多错误之处，欢迎大家提交 issues 或者 fork 代码库。 -本书采用开源工具 [gitbook][]书写完成，图示采用 等绘制，书中介绍的工具也几乎均开源软件。科学研究存在许多功利因素，所以很难有 OPEN 的条件。但至少目前有了许多开源的工具，有学习文档和资料。希望 [Open Source][] 的思想能对科研工作有所帮助。 +本书采用开源工具 [gitbook][]书写完成，图示采用 graphviz 等工具绘制，书中介绍的工具也几乎均开源软件。科学研究存在许多功利因素，所以很难有 OPEN 的条件。但至少目前有了许多开源的工具，有学习文档和资料。希望 [Open Source][] 的思想能对科研工作有所帮助。 [Linux]: http://www.linux.com/ "Linux" [Illumina]: http://www.illumina.com/ "Illumina" diff --git a/SUMMARY.md b/SUMMARY.md index 92f32d3..cad1517 100644 --- a/SUMMARY.md +++ b/SUMMARY.md @@ -20,4 +20,5 @@ * [名词解释](appendix/a3.md) * [网上资源](appendix/a4.md) * [Assembly Tools and Quality](appendix/a5.md) + * [Galaxy 配置](appendix/55_galaxy.md) diff --git a/appendix/55_galaxy.md b/appendix/55_galaxy.md new file mode 100644 index 0000000..890b60e --- /dev/null +++ b/appendix/55_galaxy.md @@ -0,0 +1,2 @@ +# 5.5 Galaxy 安装与配置 + diff --git a/appendix/a1.md b/appendix/a1.md index e69de29..70887e6 100644 --- a/appendix/a1.md +++ b/appendix/a1.md @@ -0,0 +1,5 @@ +# 测序平台 + +1. Illumina MiSeq +2. Pacbio +3. iontorrent diff --git a/appendix/a2.md b/appendix/a2.md index 8d0211f..a26464d 100644 --- a/appendix/a2.md +++ b/appendix/a2.md @@ -1,5 +1,7 @@ # Amazon EC2 教程 +## 在 Amazon EC2 建立一个运行实例 + 本地电脑如果是 Windows 系统，建议下载一个 putty 来访问连接。如是 Linux 或 Mac OSX 操作系统，则直接开一终端程序用 ssh 命令访问即可。 ### 1. 建立一个 Amazon AWS 帐号 @@ -12,3 +14,9 @@ + + +## Running docker in Amazon EC2 + +docker 是一种虚拟环境### + diff --git a/appendix/a3.md b/appendix/a3.md index 3ec0eaf..bb7032d 100644 --- a/appendix/a3.md +++ b/appendix/a3.md @@ -1,6 +1,6 @@ # 名词解释 -> 以下内容均为摘抄于网上内容，在 reference 中列出相关源。因为内容来自不同网页，已无法仔细区分每个条目来源，如果原作者不同意我将内容复制在这里，麻烦联系本人，我会对其进行删除。 +> 以下内容均为摘抄于网上内容，相关链接会在 reference 中列出。因为内容来自不同网页，已无法仔细区分每个条目来源，如果原作者不同意我将内容复制在这里，麻烦联系本人，我会对其进行删除。 **一代测序技术**：即传统的Sanger测序法，Sanger法是根据核苷酸在待定序列模板上的引物点开始，随机在某一个特定的碱基处终止，并且在每个碱基后面进行荧光标记，产生以A、T、C、G结束的四组不同长度的一系列核苷酸，每一次序列测定由一套四个单独的反应构成，每个反应含有所有四种脱氧核苷酸三磷酸(dNTP)，并混入限量的一种不同的双脱氧核苷三磷酸(ddNTP)。由于ddNTP缺乏延伸所需要的3-OH 基团，使延长的寡聚核苷酸选择性地在G、A、T或C处终止，使反应得到一组长几百至几千碱基的链终止产物。它们具有共同的起始点，但终止在不同的的核苷酸上，可通过高分辨率变性凝胶电泳分离大小不同的片段，通过检测得到DNA碱基序列。 @@ -120,6 +120,6 @@ Index：标签，在Illumina平台的多重测序（Multiplexed Sequencing）过 -### reference +### Reference 1. http://www.macrogencn.com/_d275872179.htm 2. diff --git a/appendix/a4.md b/appendix/a4.md index 695f8c7..9cb8fa4 100644 --- a/appendix/a4.md +++ b/appendix/a4.md @@ -16,7 +16,6 @@ * *[UC Davis training](http://training.bioinformatics.ucdavis.edu/)* * *[UC Texas at Austin wiki](https://wikis.utexas.edu/display/bioiteam/Home)* - ### 博客 关于生物信息学与高通量测序技术相关内容的博客网站。 * *[糗世界](http://pgfe.umassmed.edu/ou/)* @@ -39,8 +38,8 @@ * *[VFDB](http://www.mgc.ac.cn/VFs/main.htm)* 中国医学科学院病原系统生物学研究室创建的病原菌毒力基因数据库 * *[MVIRDB](http://mvirdb.llnl.gov/)* Lawrence Livermore National Laboratory 创建毒力基因整合数据库。数据来源于包括VFDB在内的多个数据库。 * *[DBETH](http://www.hpppi.iicb.res.in/btox/About_DBETH.html)* 对人致病的细菌外毒素数据库，由印度科研机构维护。 -* *[Food Microbe Tracker](http://www.foodmicrobetracker.com/login/login.aspx)* Cornell大学主持的食源性致病菌的数据库项目，主要有表型和PFGE分型资料。最大的特点可以提交自己的PFGE数据与数据库中的比对，但可能我使用不当或理解不对，比对出来的结果总是完全对不上，不知道它具体的算法。 -* +* *[Food Microbe Tracker](http://www.foodmicrobetracker.com/login/login.aspx)*S Cornell大学主持的食源性致病菌的数据库项目，主要有表型和PFGE分型资料。最大的特点可以提交自己的PFGE数据与数据库中的比对，但可能我使用不当或理解不对，比对出来的结果总是完全对不上，不知道它具体的算法 +* *[Genomespace](http://www.genomespace.org/)* 基于web界面的基因组分析工具 ### 讲座课件 在线的各种PPT讲座课件，这里选择一些基础简介的可见和一些与微生物测序内容相关的课件 diff --git a/appendix/a5.md b/appendix/a5.md index dc83704..d234ff8 100644 --- a/appendix/a5.md +++ b/appendix/a5.md @@ -11,4 +11,4 @@ * ABySS * MIRA * SOAPdenovo -* +* diff --git a/book.json b/book.json index 53b1dcb..7a503d7 100644 --- a/book.json +++ b/book.json @@ -1,12 +1,16 @@ { "plugins": [ - "disqus" + "disqus", + "ga" ], "pluginsConfig": { "disqus": { "disqus": { "shortName": "bac-ngs-book" } + }, + "ga": { + "token": "UA-55420348-1" } } -} \ No newline at end of file +} diff --git a/chapter_1/README.md b/chapter_1/README.md index bb88a8a..6fc40d4 100644 --- a/chapter_1/README.md +++ b/chapter_1/README.md @@ -1,2 +1,3 @@ -# 单基因组 +# 单基因组分析 +分析流程 diff --git a/chapter_1/annotation.md b/chapter_1/annotation.md index c797f96..447079e 100644 --- a/chapter_1/annotation.md +++ b/chapter_1/annotation.md @@ -1 +1,3 @@ # Annotation + +incoming... diff --git a/chapter_1/download_sra.md b/chapter_1/download_sra.md index e69de29..edf6ba9 100644 --- a/chapter_1/download_sra.md +++ b/chapter_1/download_sra.md @@ -0,0 +1,9 @@ +# 测序数据的获得 + +以 illumina MiSeq 数据为例，其他测序工具获得的数据会在附录中探讨。 + +1. 访问NCBI-SRA数据库(如果要研究RNA表达谱可以到GEO数据库搜索测序数据) +2. 搜索关键测获得目标 +3. 下载sra格式的文件 + +批量下载数据的方法 diff --git a/chapter_2/mapping.md b/chapter_2/mapping.md index 0f3402b..adad730 100644 --- a/chapter_2/mapping.md +++ b/chapter_2/mapping.md @@ -1,3 +1,16 @@ # mapping ### MUMmer + +1. 安装 MUMmer + +``` +$ cd ~/app +app$ wget http://nchc.dl.sourceforge.net/project/mummer/mummer/3.23/MUMmer3.23.tar.gz +app$ tar zxvf MUMmer3.23.tar.gz +app$ cd MUMmer3.23 +app$ make install +app$ sudo ln -s `pwd`/bin/* /usr/local/sbin/ +``` + +2. diff --git a/chapter_3/phy.md b/chapter_3/phy.md index c901390..412e9bd 100644 --- a/chapter_3/phy.md +++ b/chapter_3/phy.md @@ -1,2 +1,3 @@ # 进化分析与进化树绘制 +incoming... diff --git a/chapter_4/16s.md b/chapter_4/16s.md index d5fd882..f4a64c8 100644 --- a/chapter_4/16s.md +++ b/chapter_4/16s.md @@ -1 +1,3 @@ # 16s 分析种群结构 + +incoming... diff --git a/chapter_4/shotgun.md b/chapter_4/shotgun.md index 48b6b8e..9b3100f 100644 --- a/chapter_4/shotgun.md +++ b/chapter_4/shotgun.md @@ -1,3 +1,3 @@ # shotgun 测序获得病原 -upcoming... +incoming... diff --git a/node_modules/gitbook-plugin-disqus/.npmignore b/node_modules/gitbook-plugin-disqus/.npmignore new file mode 100644 index 0000000..da23d0d --- /dev/null +++ b/node_modules/gitbook-plugin-disqus/.npmignore @@ -0,0 +1,25 @@ +# Logs +logs +*.log + +# Runtime data +pids +*.pid +*.seed + +# Directory for instrumented libs generated by jscoverage/JSCover +lib-cov + +# Coverage directory used by tools like istanbul +coverage + +# Grunt intermediate storage (http://gruntjs.com/creating-plugins#storing-task-files) +.grunt + +# Compiled binary addons (http://nodejs.org/api/addons.html) +build/Release + +# Dependency directory +# Deployed apps should consider commenting this line out: +# see https://npmjs.org/doc/faq.html#Should-I-check-my-node_modules-folder-into-git +node_modules diff --git a/node_modules/gitbook-plugin-disqus/LICENSE b/node_modules/gitbook-plugin-disqus/LICENSE new file mode 100644 index 0000000..3e53c4e --- /dev/null +++ b/node_modules/gitbook-plugin-disqus/LICENSE @@ -0,0 +1,201 @@ +Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright 2014 FriendCode Inc. + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/node_modules/gitbook-plugin-disqus/README.md b/node_modules/gitbook-plugin-disqus/README.md new file mode 100644 index 0000000..1ed0e95 --- /dev/null +++ b/node_modules/gitbook-plugin-disqus/README.md @@ -0,0 +1,26 @@ +Disqus integration for GitBook +============== + +You can use install it via **NPM**: + +``` +$ npm install gitbook-plugin-disqus +``` + +And use it for your book with: + +``` +$ gitbook build ./ --plugins=disqus +``` + + +You can set the Disqus shortname using the plugins configuration (command line option: `--pluginsConfig`) with the following content: + +``` +{ + "disqus": { + "shortName": "XXXXXXX" + } +} +``` + diff --git a/node_modules/gitbook-plugin-disqus/book/plugin.js b/node_modules/gitbook-plugin-disqus/book/plugin.js new file mode 100644 index 0000000..4fd31fd --- /dev/null +++ b/node_modules/gitbook-plugin-disqus/book/plugin.js @@ -0,0 +1,34 @@ +require(["gitbook", "jQuery"], function(gitbook, $) { + var resetDisqus = function() { + var $disqusDiv = $("
", { + "id": "disqus_thread" + }); + $(".book-body .page-inner").append($disqusDiv); + + if (typeof DISQUS !== "undefined") { + DISQUS.reset({ + reload: true, + config: function () { + this.language = "en"; + this.page.url = window.location.href; + } + }); + } + } + + gitbook.events.bind("start", function(e, config) { + config.disqus = config.disqus || {}; + var disqus_shortname = config.disqus.shortName; + + /* * * DON'T EDIT BELOW THIS LINE * * */ + (function() { + var dsq = document.createElement('script'); dsq.type = 'text/javascript'; dsq.async = true; + dsq.src = '//' + disqus_shortname + '.disqus.com/embed.js'; + (document.getElementsByTagName('head')[0] || document.getElementsByTagName('body')[0]).appendChild(dsq); + })(); + + resetDisqus(); + }); + + gitbook.events.bind("page.change", resetDisqus); +}); \ No newline at end of file diff --git a/node_modules/gitbook-plugin-disqus/index.js b/node_modules/gitbook-plugin-disqus/index.js new file mode 100644 index 0000000..1fe6db4 --- /dev/null +++ b/node_modules/gitbook-plugin-disqus/index.js @@ -0,0 +1,8 @@ +module.exports = { + book: { + assets: "./book", + js: [ + "plugin.js" + ] + } +}; \ No newline at end of file diff --git a/node_modules/gitbook-plugin-disqus/package.json b/node_modules/gitbook-plugin-disqus/package.json new file mode 100644 index 0000000..fb4322c --- /dev/null +++ b/node_modules/gitbook-plugin-disqus/package.json @@ -0,0 +1,22 @@ +{ + "name": "gitbook-plugin-disqus", + "description": "Disqus integration into GitBook", + "main": "index.js", + "version": "0.0.1", + "engines": { + "gitbook": "*" + }, + "homepage": "https://github.com/GitbookIO/plugin-disqus", + "repository": { + "type": "git", + "url": "https://github.com/GitbookIO/plugin-disqus.git" + }, + "license": "Apache 2", + "bugs": { + "url": "https://github.com/GitbookIO/plugin-disqus/issues" + }, + "readme": "Disqus integration for GitBook\n==============\n\nYou can use install it via **NPM**:\n\n```\n$ npm install gitbook-plugin-disqus\n```\n\nAnd use it for your book with:\n\n```\n$ gitbook build ./ --plugins=disqus\n```\n\n\nYou can set the Disqus shortname using the plugins configuration (command line option: `--pluginsConfig`) with the following content:\n\n```\n{\n \"disqus\": {\n \"shortName\": \"XXXXXXX\"\n }\n}\n```\n\n", + "readmeFilename": "README.md", + "_id": "gitbook-plugin-disqus@0.0.1", + "_from": "gitbook-plugin-disqus@*" +} diff --git a/package.json b/package.json index 5a42371..56fb89d 100644 --- a/package.json +++ b/package.json @@ -2,6 +2,7 @@ "name": "book", "version": "0.0.0", "dependencies": { - "gitbook-plugin-disqus": "*" + "gitbook-plugin-disqus": "*", + "gitbook-plugin-ga": "*" } } \ No newline at end of file diff --git a/ready.md b/ready.md index 4e7e2e6..0646f43 100644 --- a/ready.md +++ b/ready.md @@ -47,10 +47,11 @@ $ sudo apt-get remove python-dev # 删除python-dev 有兴趣的生物学家可以先阅读以下资料，增强对 Unix 的相关知识： 1. [Unix and Perl Primer for Biologists](http://korflab.ucdavis.edu/Unix_and_Perl/current.html) +2. [The Linux Command Line](http://billie66.github.io/TLCL/book/zh/)S ## 我实在学不会 Linux，有没有别的方案？ -对于实在不喜学习命令行工具但仍想自己分析数据的，推荐尝试 [Orione][] 工具。这是一个基于 Galaxy （最主流的基于 web 的免费生物数据分析平台） 的微生物高通量测序数据分析框架，里面集成了常见的微生物数据分析工具，各种测序应用的分析工作流。 [Orione][] 的文档参考[这里](http://orione-documentation.readthedocs.org/)，想研究代码参考[这里](https://bitbucket.org/crs4/orione-tools)。 +对于实在不喜学习命令行工具但仍想自己分析微生物数据的，推荐尝试 [Orione][] 工具。这是一个基于 Galaxy （最主流的基于 web 的免费生物数据分析平台） 的微生物高通量测序数据分析框架，里面集成了常见的微生物数据分析工具，各种测序应用的分析工作流。 [Orione][] 的文档参考[这里](http://orione-documentation.readthedocs.org/)，想研究代码参考[这里](https://bitbucket.org/crs4/orione-tools)。 对于可以接受购买商业化产品的用户，希望带 GUI 的本地软件用户，可以考虑购买 [CLC workbench](http://www.clcbio.com/products/clc-genomics-workbench/) S