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• pvg09

[pvg09]

Contact

If you need help with installing and running Swift, please contact Pankaj Gupta at pankaj.gupta@stjude.org.

[pvg09]

Hardware and software requirements

• Linux OS
• 4 GB of system memory
• CUDA compatible graphics card
• CUDA toolkit 4.2 or later
• 6 GB of global memory on GPU
• 49 KB of shared memory on GPU

[pvg09]

Installation

1. Download the tarball
2. Untar the tarball:
   
   $ tar -xvzf swift-x.y.z.tar.gz
3. Change to the directory containing the source code:
   
   $ cd /path/to/swift-x.y.z
4. Compile the code:
   
   $ make
5. Open 'src/common.h' file and change the value of TMP_DIR macro appropriately. Make sure the directory specified in TMP_DIR macro exists.

[pvg09]

Running Swift

$ /path/to/swift -q \<query fasta file> -r \<reference fasta file> -o \<output file>

Optional parameters:

-q2  \<string\>   Paired query fasta file
-l   \<int\>      Length of seed (Default: 12)
-m   \<int\>      Match score (Default: 2)
-M   \<int\>      Mismatch score (Default: -1)
-O   \<int\>      Gap open penalty (Default: -10)
-E   \<int\>      Gap extension penalty (Default: -1)
-t   \<int\>      Threshold value to ignore reference repeats
-cpu            Run program on CPU only
-f   \<int\>      Output format:
                0 - Default alignment output format. Output includes alignment, score, positions, and length.
                1 - SAM format
-v              Print program version
-h              Print usage
</int\></int\></int\></int\></int\></int\></int\></string\>

[pvg09]

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.