I downloaded the source and it was the easiest build ever. Just cd into the project directory and do
Remember to make sym links. Then, before using it I need to build an index for the reference genome:
Take it out for a spin:
Virtually instantaneous! The
I's are made-up quality scores (since this is a FASTA file using option
-f, and it doesn't have them).
Some other options:
--refout prints to a file
--quiet what it says
-m 1 if a read has more than 1 match, do not report it
--suppress(doesn't seem to work with
--refout), but we can just redirect the output:
Let's time it on a bigger input file:
Compare with BLAT:
13 seconds v. 25 seconds (roughly). However, Bowtie is doing a lot more I/O.
BLAT has more hits.
That would certainly bear investigation. But Bowtie definitely looks like a winner.