周六考试（二）

有用的网站：

大盘鸡
赞哥
亚磊
Quicl's Blog
Genome Size Estimation
Kmer分析
考题

1. 软件下载地址：
   a. vcftools

     wget https://nchc.dl.sourceforge.net/project/vcftools/vcftools_0.1.13.tar.gz
   

   使用：
   1. pele' blog
   2. vcftools使用
   b. SOAPdenovo2
   https://jaist.dl.sourceforge.net/project/soapdenovo2/SOAPdenovo2/src/r240/SOAPdenovo2-src-r240.tgz
   注意在以下文件加入文本：

仔细查看编译输出，发现有如下几个错误提示：

multi_threads.cpp:93:14: error: ‘usleep’ was not declared in this scope

build_preArc.cpp:1071:39: error: ‘usleep’ was not declared in this scope

pregraph_sparse.cpp:171:42: error: ‘usleep’ was not declared in this scope

pregraph_sparse.cpp:504:2: error: ‘optind’ was not declared in this scope

pregraph_sparse.cpp:507:64: error: ‘getopt’ was not declared in this scope

于是找到这些源码，在头文件中加入：

#include “unistd.h“

c. jellyfish
https://github.com/gmarcais/Jellyfish/releases

Installation

./configure --prefix=$HOME
make -j 4
make install

d. SOAPec v2.01
里面有Kmer_Freq_AR