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Bowtie2

Bowtie 2 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.

Note

This is an autogenerated page, more detail including examples may be available for this package. Please see the first section of Software on Stanage

After connecting to Stanage (see Establishing a SSH connection), start an interactive session with the following command:

srun --pty bash -i

A version of Bowtie2 can then be made available with one of the following:

module load Bowtie2/2.4.5-GCC-11.3.0

Notes

Bowtie2 was installed using Easybuild, build details can be found in $EBROOTBOWTIE2/easybuild with a given module loaded.

Direct dependencies for latest version of Bowtie2