在Ubuntu环境中设置Bowtie

**什么是Bowtie？What is Bowtie？**

[Bowtie](http://bowtie-bio.sf.net/) is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. It aligns 35-base-pair reads to the human genome at a rate of 25 million reads per hour on a typical workstation. Bowtie indexes the genome with a [Burrows-Wheeler](http://en.wikipedia.org/wiki/Burrows-Wheeler_transform) index to keep its memory footprint small: for the human genome, the index is typically about 2.2 GB (for unpaired alignment) or 2.9 GB (for paired-end or colorspace alignment). Multiple processors can be used simultaneously to achieve greater alignment speed. Bowtie can also output alignments in the standard [SAM](http://samtools.sourceforge.net/SAM1.pdf) format, allowing Bowtie to interoperate with other tools supporting SAM, including the [SAMtools](http://samtools.sourceforge.net/) consensus, SNP, and indel callers. Bowtie runs on the command line under Windows, Mac OS X, Linux, and Solaris. [Bowtie](http://bowtie-bio.sf.net/) also forms the basis for other tools, including [TopHat](http://tophat.cbcb.umd.edu/): a fast splice junction mapper for RNA-seq reads, [Cufflinks](http://cufflinks.cbcb.umd.edu/): a tool for transcriptome assembly and isoform quantitiation from RNA-seq reads, [Crossbow](http://bowtie-bio.sf.net/crossbow): a cloud-computing software tool for large-scale resequencing data,and [Myrna](http://bowtie-bio.sf.net/myrna): a cloud computing tool for calculating differential gene expression in large RNA-seq datasets.

简而言之，Bowtie是分析比对高通量（下一代）测序技术数据的一个工具软件。

**Bowtie的安装**

\[bash\]sudo apt-get install bowtie\[/bash\]

**设置Bowtie的Index所在位置**

\[bash\]gedit \~/.bashrc\[/bash\]

在其中添加一行（请根据实际情况修改文件夹名称）：

\[bash\]export BOWTIE\_INDEXES=”\~/bowtie-index”;\[/bash\]

保存、关闭gedit。

重新读取设置：\[bash\]source \~/.bashrc\[/bash\]

这时运行：\[bash\]export\|grep BOWTIE\[/bash\]

会得到BOWTIE\_INDEXES的变量设置情况。以后既可以将Bowtie运行所需要的Index文件下载下来（或者自己生成）放置到该文件夹中。