Bowtie¶

Description¶

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end). * BOWTIE_INDEXES - indexes directory

Environment Modules¶

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

Environment Variables¶

HPC_BOWTIE_DIR - installation directory
HPC_BOWTIE_BIN - executable directory
HPC_BOWTIE_DOC - documents directory
HPC_BOWTIE_EX - examples directory
HPC_BOWTIE_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