====== Bowtie and Bowtie2 ======
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  * **BOWTIE**
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<code>
# apt-get install bowtie
</code>
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<code>
$ bowtie --version

bowtie version 1.1.2
64-bit
Built on lgw01-11
Thu Nov 26 11:11:48 UTC 2015
Compiler: gcc version 5.2.1 20151123 (Ubuntu 5.2.1-25ubuntu1)
Options: -O3  -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-Bsymbolic-functions -Wl,-z,relro
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

</code>
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  * **BOWTIE2**
Fast and sensitive read alignment
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  * Download

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<code>
wget https://netix.dl.sourceforge.net/project/bowtie-bio/bowtie2/2.2.9/bowtie2-2.2.9-linux-x86_64.zip
unzip bowtie2-2.2.9-linux-x86_64.zip
</code>
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  * Install
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<code>
mv bowtie2-2.2.9 /usr/local/bin/ 
ln -s /usr/local/bin/bowtie2-2.2.9/bowtie2 /usr/local/bin/
ln -s /usr/local/bin/bowtie2-2.2.9/bowtie2-build /usr/local/bin/
ln -s /usr/local/bin/bowtie2-2.2.9/bowtie2-inspect /usr/local/bin/
chown -R root:root /usr/local/bin/bowtie2-2.2.9

# apt-get install libtbb-dev
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  * Check
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<code>
$ bowtie2 --version

/usr/local/bin/bowtie2-2.2.9/bowtie2-align-s version 2.2.9
64-bit
Built on localhost.localdomain
Thu Apr 21 18:36:37 EDT 2016
Compiler: gcc version 4.1.2 20080704 (Red Hat 4.1.2-54)
Options: -O3 -m64 -msse2  -funroll-loops -g3 -DPOPCNT_CAPABILITY
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
</code>
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**NOTE**
Tophat2 v2.1.1 test_data error with bowtie2 v2.3.0