The Swift sequence alignment tool is described in detail in:

Rasmussen, K. R., Stoye, J., and Myers, E. W.,
"Efficient q-Gram Filters for Finding All ε-Matches over a Given Length",
In Proc. of the 9th Conf. on Computational Molecular Biology (RECOMB'05),
pp189-203, Cambridge, MA, 2005.

These package contains the sources for Swift.
Kim Rasmussen put the project  under the MIT
license, so you are free to modify and redistribute, as long as you
don't remove the copyright notices.

== Installation ==
To install extract the archive and change into the directory
e.g.
tar xfz swift*tar.gz && cd swift*
Then create a new directory "build" and change to it:
mkdir build && cd build
Then it is time to configure and compile:
cmake .. && make
If everything goes well you will have the swift binary at
swift/swift.
(Maybe you want to install it: make install
You can change the install prefix with
ccmake .
)


== Using ==
To use the tool you have to create a database for query/queries and
target and create a q-gram index for both. Query and target should be in
(multiple) fasta format.

swift create query many_queries.fasta
swift index query --gram 11


swift create database some_target.fasta
swift index database --gram 11

At this point you can query the database; e.g.:
swift query --maxerror 0.01 --minlen 500 --gram 11 database query
--output query.csv


