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.
Alignment using bowtie2 is a 2-step process - indexing the reference genome, followed by aligning the sequence data.
Create indexes of your reference genome of interest stored in
bowtie2-build [option(s)] <reference.fasta> <bt2-index-basename>
This will create new files with the provided basename and extensions
These files constitute the index.
Align paired-end reads
sampleR2.fqto the reference genome indexed in the previous step, using
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
For more information, please refer to the Bowtie2 [manual] (http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml).
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