QIIME pipeline 采用fastq-join 和 SeqPrep 合并Illumina paired-end reads。其安装方法如下：

Currently, there are two methods that can be selected by the user to join paired-end data:

1. fastq-join - Erik Aronesty, 2011. ea-utils : “Command-line tools for processing biological sequencing data” (http://code.google.com/p/ea-utils)

2. SeqPrep - (https://github.com/jstjohn/SeqPrep)

安装：fastq-join

(1)下载fastq-join，并解压缩

https://drive.google.com/folderview?id=0B7KhouP0YeRAOTFWWGVFYkFSQjg&usp=sharing

(2)cd 软件目录

(3)sudo make

(4)sudo make install (自动将可执行文件加入Path)

安装：SeqPrep

(1)打开terminal;

(2)git clone https://github.com/jstjohn/SeqPrep.git 

(3)cd 软件目录

(4)sudo make

(5)sudo make install (自动将可执行文件加入Path)