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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


  • 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)

colorspace indexing

A big advantage of this first version of bowtie is its ability to handle colorspace fastq files. For this, a special index of the reference sequence must be generated, using bowtie-build and the special option -C. The rest of the command is the same, and you would of course use a different label for later processing with colorspace files.

Here is an example for an M. abscessus reference:

bowtie-build -C NC_010397.fasta NC397_cspace

Note that no other index files should get overwritten, so that different index files can coexist in the same directory.

the alignment step

We shall deal with colorspace files here, because there is only an added -C in the options for them, and so it can be ommited when they are not colorspace files. Here is an template for such a command:

bowtie -S -C <label_for_index_of_reference> <uncompressed_fastq_filename> <output_filename_with_sam_extension>

For example, in one recent run:

bowtie -S -C mabsref SRR1501363_.fastq bwt363go.sam

As you can see, the final two arguments are not marked by an ption, so always must be the uncompressed input fasta file and the output sam.