Bowtie2¶

Description¶

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. * BOWTIE2_INDEXES - indexes directory

Environment Modules¶

Run module spider bowtie2 to find out what environment modules are available for this application.

Environment Variables¶

HPC_BOWTIE2_DIR - installation directory
HPC_BOWTIE2_BIN - executable directory
HPC_BOWTIE2_DOC - documents directory
HPC_BOWTIE2_EXE - examples directory
HPC_BOWTIE2_SCR - scripts directory

Additional Usage Information¶

Note

If your data is compressed, your job script should add another CPU core to the job resource request to accommodate the external gzip process that bowtie will run.

Categories¶

biology, ngs, sequencing