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).

Versions and Availability

Module Names for bowtie on philip
Machine Version Module Name
philip 1.1.1 bowtie/1.1.1/INTEL-15.0.3
philip 2.1.0 bowtie2/2.1.0/INTEL-15.0.3
▶ **FIX-ME** FAQ?


bowtie --help  for command line options

e.g., bowtie -c prefix-index-file GCGTGAGCTATGAGAAAGCGCCACGCTTCC
      bowtie prefix-index-file reads.fq

      bowtie-build seq.fna index-file  


Last modified: June 20 2015 11:20:48.