什么是Bowtie？What is Bowtie？
Bowtie 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 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 format, allowing Bowtie to interoperate with other tools supporting SAM, including the SAMtools consensus, SNP, and indel callers. Bowtie runs on the command line under Windows, Mac OS X, Linux, and Solaris.
Bowtie also forms the basis for other tools, including TopHat: a fast splice junction mapper for RNA-seq reads, Cufflinks: a tool for transcriptome assembly and isoform quantitiation from RNA-seq reads, Crossbow: a cloud-computing software tool for large-scale resequencing data,and Myrna: a cloud computing tool for calculating differential gene expression in large RNA-seq datasets.
If you use Bowtie for your published research, please cite the Bowtie paper.
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。
如此这般，既可以使用Bowtie了。如果使用Bowtie时发生内存不够的错误，多加点内存吧，别无他法。