====== Bowtie2 & Tophat2 (from binary) ======
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  * **BOWTIE2**
Fast and sensitive read alignment
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  * Download

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<code>
wget http://garr.dl.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-linux-x86_64.zip 
unzip bowtie2-2.1.0-linux-x86_64.zip
</code>
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  * Install
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<code>
mv bowtie2-2.1.0 /usr/local/bin/ 
ln -s /usr/local/bin/bowtie2-2.1.0/bowtie2 /usr/local/bin/
ln -s /usr/local/bin/bowtie2-2.1.0/bowtie2-build /usr/local/bin/
ln -s /usr/local/bin/bowtie2-2.1.0/bowtie2-inspect /usr/local/bin/
ln -s /usr/local/bin/bowtie2-2.1.0/bowtie2-align /usr/local/bin/
chown -R root:root /usr/local/bin/bowtie2-2.1.0 
</code>
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  * **TOPHAT2**
A spliced read mapper for RNA-Seq.
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  * Download

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<code>
wget http://tophat.cbcb.umd.edu/downloads/tophat-2.0.13.Linux_x86_64.tar.gz 
tar xvfz tophat-2.0.13.Linux_x86_64.tar.gz 
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  * Install
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<code>
mv tophat-2.0.13.Linux_x86_64 /usr/local/bin/ 
ln -s /usr/local/bin/tophat-2.0.13.Linux_x86_64/tophat2 /usr/local/bin/
chown -R root:root /usr/local/bin/tophat-2.0.13.Linux_x86_64  
</code>
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  * Test
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<code>
wget http://tophat.cbcb.umd.edu/downloads/test_data.tar.gz 
tar zxvf test_data.tar.gz 
cd test_data/
tophat2 -r 20 test_ref reads_1.fq reads_2.fq 
</code>
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