Swift Sequence Alignment Program Wiki
GPU-based DNA sequence alignment program using Smith-Waterman
Status: Alpha
Brought to you by:
pvg09
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Contact
If you need help with installing and running Swift, please contact Pankaj Gupta at pankaj.gupta@stjude.org.
Last edit: pvg09 2012-05-30
Hardware and software requirements
Last edit: pvg09 2012-09-10
Installation
$ tar -xvzf swift-x.y.z.tar.gz
$ cd /path/to/swift-x.y.z
$ make
Last edit: pvg09 2012-05-30
Running Swift
$ /path/to/swift -q \<query fasta file> -r \<reference fasta file> -o \<output file>
Optional parameters:
Last edit: pvg09 2012-05-30
FAQ
Q: Is there a limit on the number of reference sequences that can be used in Swift?
A: Yes, currently Swift supports 25 or so reference sequences due to memory limitations on the GPU.
Q: Is there a limit on the size of each reference sequence?
A: No, there is no limit on the size of each reference sequence. However, there is a limit on the number of reference sequences.
Q: What Operating Systems is Swift available for?
A: Currently Swift is available for Linux OS only.
Q: Under what license is Swift available?
A: Swift is available under GPLv2 license.
Last edit: pvg09 2012-11-07