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Bioinformatics, Aligner


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.

Available versions (Euler, old software stack)

Legacy versions Supported versions New versions

Environment modules (Euler, old software stack)

Version Module load command Additional modules loaded automatically
2.2.3 module load gcc/4.8.2 bowtie2/2.2.3

How to submit a job

You can submit a bowtie2 job in batch mode with the following command:
bsub [LSF options] "bowtie2 [bowtie2 options]"
Here you need to replace [bowtie2 options] with bowtie2 command line options (please run bowtie2 -h for getting a list of all command line options) and [LSF options] with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of bsub on the wiki page about the batch system.

License information