jellyfish kmer_assembly (NEKTAR) 打碎再组装

./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

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