SOAPdenovo2是用于序列组装的常用软件，其可在GitHub上下载并进行安装，网站为：https://github.com/aquaskyline/SOAPdenovo2

一、安装

使用git下载,使用make进行编译

git clone https://github.com/aquaskyline/SOAPdenovo2.git
cd SOAPdenovo2
make

这里安装比较简单，我就不多说了，如果遇到问题可在github issues上查看是否有解答。

二、使用

2.1、构建配置文件

SOAPdenovo2的使用需要手动构建一个配置文件，在安装好的软件目录有示例配置文件（见图2-1），直接将其配置文件复制过来再进行修改即可。其中配置文件中分为全局配置和文库配置，max_rd_len是唯一的一个全局配置参数，任何长度超过该参数的序列都会被截取到该长度。下面是官方对主要参数的一个解释。

1) avg_ins
   This value indicates the average insert size of this library or the peak value position in the insert size distribution figure.
2) reverse_seq
   This option takes value 0 or 1. It tells the assembler if the read sequences need to be complementarily reversed.
Illumima GA produces two types of paired-end libraries: a) forward-reverse, generated from fragmented DNA ends with typical insert size less than 500 bp; b) reverse-forward, generated from circularizing libraries with typical insert size greater than 2 Kb. The parameter "reverse_seq" should be set to indicate this: 0, forward-reverse; 1, reverse-forward.
3) asm_flags
   This indicator decides in which part(s) the reads are used. It takes value 1(only contig assembly), 2 (only scaffold assembly), 3(both contig and scaffold assembly), or 4 (only gap closure).
4) rd_len_cutof
   The assembler will cut the reads from the current library to this length.
5) rank
   It takes integer values and decides in which order the reads are used for scaffold assembly. Libraries with the same "rank" are used at the same time during scaffold assembly.
6) pair_num_cutoff
   This parameter is the cutoff value of pair number for a reliable connection between two contigs or pre-scaffolds. The minimum number for paired-end reads and mate-pair reads is 3 and 5 respectively.
7) map_len
   This takes effect in the "map" step and is the minimun alignment length between a read and a contig required for a reliable read location. The minimum length for paired-end reads and mate-pair reads is 32 and 35 respectively.

图2-1：示例配置文件部分截图

2.2、运行

构建好配置文件后，即可开始运行组装程序了，运行可分为两种模式，一种是分步运行，一种是一键式运行。这里建议直接用一键式运行的方式比较简单快捷。假设我们使用k-mer 63 进行组装，则其运行脚本为

SOAPdenovo-63mer all -s config_file -K 63 -R -o graph_prefix 1>ass.log 2>ass.err

运行结束后，其结果中有两个文件比较重要，一个是后缀为contig，其中包含了contig序列；一个是后缀为scafSeq，其中包含了scaffold 序列。如果你想了解组装的N50等信息，可以直接查看生成的ass.log文件。

参考：

1. https://github.com/aquaskyline/SOAPdenovo2