1.PBJelly2 简介

PBJelly2 用于利用 Pacbio 数据进行基因组补洞和 scaffold 连接。

2.安装 PBJelly2

安装 HDF：
$ wget http://www.hdfgroup.org/ftp/HDF5/current/bin/linux-centos6-x86_64/hdf5-1.8.15-patch1-linux-centos6-x86_64-shared.tar.gz
$ tar zxf hdf5-1.8.15-patch1-linux-centos6-x86_64-shared.tar.gz
$ mv hdf5-1.8.15-patch1-linux-centos6-x86_64-shared /opt/biosoft/hdf5-1.8.15-patch1
$ export HDF5INCLUDEDIR=/opt/biosoft/hdf5-1.8.15-patch1/include/
$ export HDF5LIBDIR=/opt/biosoft/hdf5-1.8.15-patch1/lib/
$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/biosoft/hdf5-1.8.15-patch1/lib/
$ export C_INCLUDE_PATH=$C_INCLUDE_PATH:/opt/biosoft/hdf5-1.8.15-patch1/include/

安装 Blasr（需求 HDF v1.8.0或以上版本）：
$ wget https://github.com/PacificBiosciences/blasr/archive/master.zip -O blasr.zip
$ unzip blasr.zip
$ mv blasr-master/ /opt/biosoft/blasr
$ cd /opt/biosoft/blasr
$ make -j 8
$ echo 'PATH=$PATH:/opt/biosoft/blasr/alignment/bin/' >> ~/.bashrc

安装Python模块 Networkx v1.7
$ wget https://pypi.python.org/packages/source/n/networkx/networkx-1.7.tar.gz
$ tar zxf networkx-1.7.tar.gz
$ cd networkx-1.7
$ sudo /usr/local/bin/python setup.py install

安装Python模块 pyparsing
$ wget https://pypi.python.org/packages/source/p/pyparsing/pyparsing-2.0.3.tar.gz
$ tar zxf pyparsing-2.0.3.tar.gz
$ cd pyparsing-2.0.3
$ sudo /usr/local/bin/python setup.py install

安装Python模块 numpy
$ wget https://pypi.python.org/packages/source/n/numpy/numpy-1.9.2.tar.gz
$ tar zxf numpy-1.9.2.tar.gz 
$ cd numpy-1.9.2
$ sudo /usr/local/bin/python setup.py install

安装Python模块 h5py
$ wget https://pypi.python.org/packages/source/h/h5py/h5py-2.5.0.tar.gz
$ cd h5py-2.5.0
$ export LIBRARY_PATH=/opt/biosoft/hdf5-1.8.15-patch1/lib/:$LIBRARY_PATH
$ /usr/local/bin/python setup.py build
$ sudo /usr/local/bin/python setup.py install

安装Python模块 pysam
$ https://pypi.python.org/packages/source/p/pysam/pysam-0.8.3.tar.gz
$ tar zxf pysam-0.8.3.tar.gz 
$ cd pysam-0.8.3
$ sudo /usr/local/bin/python setup.py install

安装Python模块 intervaltree
$ wget https://pypi.python.org/packages/source/i/intervaltree/intervaltree-2.0.4.tar.gz
$ tar zxf intervaltree-2.0.4.tar.gz
$ cd intervaltree-2.0.4
$ sudo /usr/local/bin/python setup.py install

安装 PBJelly2
$ wget http://sourceforge.net/projects/pb-jelly/files/latest/download -O PBSuite.tar.gz
$ tar zxf PBSuite.tar.gz -C /opt/biosoft/
$ SWEETPATH=`ls /opt/biosoft/PBSuite* -d`
$ echo "perl -p -i -e 's#export SWEETPATH=.*#export SWEETPATH=$SWEETPATH#' $SWEETPATH/setup.sh" | sh
$ echo "source $SWEETPATH/setup.sh" >> ~/.bashrc

3. 使用 PBJelly2 进行补洞

首先创建配置文件 Protocol.xml，内容如下:

<jellyProtocol>
    <reference>基因组fasta文件的路径</reference>  
    <outputDir>输出文件路径</outputDir>
    <blasr>-minMatch 8 -minPctIdentity 70 -bestn 1 -nCandidates 20 -maxScore -500 -nproc 24 -noSplitSubreads</blasr>
    <input baseDir="输入Pacbio数据文件所在的文件夹">
        <job>Pacbio数据文件名称</job>
    </input>
</jellyProtocol>

然后依次运行下6步：

$ Jelly.py setup Protocol.xml
$ Jelly.py mapping Protocol.xml
$ Jelly.py support Protocol.xml
$ Jelly.py extraction Protocol.xml
$ Jelly.py assembly Protocol.xml -x "--nproc=24"
$ Jelly.py output Protocol.xml

--nproc 参数设置运行线程数。

输出结果文件为 jelly.out.fasta 。

4. 使用 PBJelly2 进行 scaffold 连接