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  • pvg09

    pvg09 - 2012-05-09

    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
  • pvg09

    pvg09 - 2012-05-30

    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
     
    Last edit: pvg09 2012-09-10
  • pvg09

    pvg09 - 2012-05-30

    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.
     
    Last edit: pvg09 2012-05-30
  • pvg09

    pvg09 - 2012-05-30

    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

     
    Last edit: pvg09 2012-05-30
  • pvg09

    pvg09 - 2012-11-07

    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

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