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Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.


Usage on Bridges-2

To see what versions of Bowtie2 are available and if there is more than one, which is the default, along with some help, type

module spider bowtie2

To use Bowtie2, include a command like this in your batch script or interactive session to load the Bowtie2 module: (note ‘module load’ is case-sensitive):

module load bowtie2