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

Output files will have the extension ebwt.