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metagenome's Introduction

宏基因组分析流程

Metagenome analysis pipeline

目录说明

  • denovo1 # 宏基因组分析流程无参第一版 makefile格式
  • train1903 # 易生信2019年3月培训教程和代码
  • train1906 # 易生信2019年6月培训教程和代码

一、分析准备工作

Data pre-treatment

# 系统要求 System: Linux Ubuntu 18.04 / CentOS 7
# 依赖软件 Sofware: Rstudio server 1.2、KneadData v0.6.1、MetaPhlAn2 v2.7.5、HUMAnN2 v0.11.2 ......
# Windows/Linux访问Rstudio服务器，推荐使用Chrome浏览器，可选Edge，IE有兼容问题
  • fastqc 0.11.5 对所有原始序列进行质量评估
  • multiqc 1.4 汇总多样品质量评估报告

1.1 了解工作目录和文件

1.2 FastQC质量评估(可选)

1.3 序列质控和去宿主 Qaulity control and remove host contamination

1.4 质控后质量再评估 (可选)

二、宏基因组有参分析流程

Reference-based Metagenomic Pipeline (HUMAnN2)

2.1 合并质控文件为HUMAnN2输入

2.2 HUMAnN2计算物种和功能组成

2.3 物种组成表

2.4 功能组成分析

2.5 GraPhlAn图

2.6 LEfSe差异分析和Cladogram

2.7 kraken2基于NCBI数据库注释reads层面

三、宏基因组无参分析流程

De novo Metagenomic Pipeline (MEGAHIT)

3.1 拼接 Assembly

3.2 基因注释和定量 Gene annotation & quantitfy

3.3 功能基因注释

四、挖掘单菌基因组/分箱

Binning (MetaWRAP)

  • 官方测试数据

4.1 运行三种bin软件

4.2 Bin提纯

4.3 Bin定量

4.4 Bin注释

metagenome's People

Contributors

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Forkers

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