Bowtie

Introduction

This article refers to the early version of bowtie, which in fact has a few features that version 2 does not have, such as colorspace data processing

Indexing the reference

This is done using the bowtie-build command and the input reference with the second argument being a label for the output files. It is an easy command, no options are required. Here is an example:

bowtie-build NC_002127.fna e_coli_O157_H7

Explanation:

• bowtie-build is indexing creation tol of bowtie
• in this example NC_002127.fna is our reference and is the first argument
• the second argument is a label for the output index files, in this case e_coli_O157_H7
• The extensions of the output files will have the extension ebwt. The root name will be the label mentioned above with some changing added characters.