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 (1, 2, 3, 4, rev.1, rev.2)