Bowtie2 is a memory-efficient tool for aligning short sequences to long reference genomes.
It indexes the genome using FM Index, which is based on Burrows-Wheeler Transform algorithm,
to keep its memory footprint small. Bowtie2 supports gapped, local and paired-end alignment modes.
Alignment to a known reference using Bowtie2 is often an essential first step in a myriad of NGS analyses workflows.

Bowtie2 Usage

Alignment using bowtie2 is a 2-step process - indexing the reference genome, followed by aligning the sequence data.

1. Create indexes of your reference genome of interest stored in reference.fasta file:

    bowtie2-build [option(s)] <reference.fasta> <bt2-index-basename>
   

   This will create new files with the provided basename and extensions .1.bt2, .2.bt2, .3.bt2 and
   .4.bt2, .rev.1.bt2 and .rev.2.bt2.

   These files constitute the index.

2. Align paired-end reads sampleR1.fq and sampleR2.fq to the reference genome indexed in the previous step, using N cores:

    bowtie2 -x <bt2-index-basename> -1 <sampleR1.fq> -2 \
   
    <sampleR2.fq> -p <N> -S <output.sam>
   

The alignment results in SAM format are written to the file output.sam

More Information

For more information, please refer to the Bowtie2 manual.

Citation

If you use bowtie2 for your work, please cite:

Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359