Bowtie on Helix

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 was developed by Langmead et al at the University of Maryland. Bowtie reference

Programs location

/usr/local/bowtie

Programs: bowtie-build, bowtie, bowtie-maqconvert, bowtie-inspect, bowtie-maptool

Version

Type '/usr/local/bowtie/bowtie --version' on helix.

How To Use

All examples below are using the e_coli index that can be copied from /usr/local/bowtie/indexes:

% cp -r /usr/local/bowtie/indexes /home/users/bowtie/

Example 1

% cd /home/users/bowtie

% /usr/local/bowtie/bowtie -a -v 2 e_coli --concise -c ATGCATCATGCGCCAT

1-:<0,148810,2>
1-:<0,2852852,1>
1-:<0,4930433,2>
1-:<0,905664,2>
1+:<0,1093035,2>
Reported 5 alignments to 1 output stream(s)

Example 2

% /usr/local/bowtie/bowtie -k 3 -v 2 e_coli --concise -c ATGCATCATGCGCCAT
1-:<0,148810,2>
1-:<0,2852852,1>
1-:<0,4930433,2>
Reported 3 alignments to 1 output stream(s)

Documentation

http://bowtie-bio.sourceforge.net/manual.shtml

Helix Systems Scientific Supercomputing at the NIH