测序比对的方法——bowtie

此处仅记录用法，详细步骤查看官方文件：https://github.com/BenLangmead/bowtie/blob/master/MANUAL
bowtie简介

[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 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.

1.建立索引

bowtie-build GRCh38.primary_assembly.genome.fa human1

得到文件如下：

-rw-r--r-- 1 med-zhouh med-chenh 808M Jun 27 16:06 human1.1.ebwt
-rw-r--r--