https://github.com/gmarcais/Jellyfish/releases
下载https://github.com/gmarcais/Jellyfish/releases/download/v2.2.3/jellyfish-2.2.3.tar.gz
./configure --prefix=$HOME // <--enable-python-binding 可选>
make -j 4
make install
将bin下jellyfish加入环境路径中即可, PKG_CONFIG_PATH加入~/.bashrc
https://github.com/iric-soft/nektar
下载整个包，
Requirements
gcc/4.9.3 jellyfish/2.2.3 python/2.7.6
for kmer_assembly: ulimit -s unlimited
nektar-master下有3个文件呀fmindex, nektar_cpp, nektar_py
在fmindex下，执行./install.sh
在nektar_cpp下，执行 make -f Makefile.linux
将nektar_cpp下，kmer_assembly加入环境路径中，
(其实就是自己的/root/biosoft/myBin中加入软链接，再把myBin加入到.bash_profile的路径中
PATH=$PATH:/root/biosoft/myBin)
修改.bashrc,主要添加boost和python2.7.6的库路径，（原centos为python2.7.4，另外路径装了python2.7.6）
export LD_LIBRARY_PATH=/root/soft/python2/include/python2.7:/root/soft/boost/lib:/usr/local/lib:/usr/local/lib64/:$LD_LIBRARY_PATH
export C_INCLUDE_PATH=/root/soft/python2/include/python2.7:/usr/local/include/:$C_INCLUDE_PATH
export CPLUS_INCLUDE_PATH=/root/soft/python2/include/python2.7:/root/soft/boost/include:/usr/local/include/:$CPLUS_INCLUDE_PATH
export LIBRARY_PATH=/root/soft/python2/include/python2.7:/root/soft/boost/lib:$LIBRARY_PATH
export PKG_CONFIG_PATH=/root/biosoft/jellyfish/lib/pkgconfig:$PKG_CONFIG_PATH
测试test.fq两条数据
jellyfish count -m 33 -s 10G -t 4 test.fq 生成mer_counts.jf
jellyfish dump -c mer_counts.jf > kmer_count.tsv (需加一空行头）
awk '{gsub(" ","\t"); print $0}' kmer_count.tsv > kmer_count_tab.tsv (空格分隔，替换为tab分隔）
运行kmer_assembly -k kmer_count_tab.tsv -o OutDir -p mer_counts.jf (感觉随便给就行，待调查), 在OutDir文件中产生assembly.fasta和assembly.tab
