Bowtie2 on Ivy Linux VM

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 detailed information, please refer to the Bowtie2 [manual] (


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