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Swift Sequence Alignment Program download for Linux

Free download Swift Sequence Alignment Program Linux app to run online in Ubuntu online, Fedora online or Debian online

This is the Linux app named Swift Sequence Alignment Program whose latest release can be downloaded as swift-0.11.2.tgz. It can be run online in the free hosting provider OnWorks for workstations.

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Swift Sequence Alignment Program


DESCRIPTION

Swift is a DNA sequence alignment program that produces gapped alignment using the Smith-Waterman algorithm. It takes in a query file (FASTA format) and a reference file (FASTA format) as input. It outputs the reference name, read name, gapped alignment, alignment score, alignment start and end positions, and alignment length.

I gave a talk on Swift in the GPU Technology Conference 2012. The talk can be accessed at http://www.gputechconf.com/gtcnew/on-demand-GTC.php?sessionTopic=58&searchByKeyword=&submit=&select=+&sessionEvent=&sessionYear=&sessionFormat=#1303.

To install and run Swift, please refer to the Wiki page: http://sourceforge.net/p/swiftseqaligner/wiki/Home/

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



Features

  • Produces gapped alignment using Smith-Waterman algorithm
  • Smith-Waterman algorithm runs on the GPU (Graphics Processing Unit)
  • Accepts a read file (FASTA format) and a reference file (FASTA format) as inputs
  • Outputs reference name, read name, gapped alignment, alignment score, alignment start and end positions, and alignment length
  • Supports Illumina reads (fixed length)
  • Requirements: Linux OS; 4 GB system memory; CUDA capable graphics card; CUDA toolkit 4.2+; 6 GB global memory; 49 KB shared memory


Audience

Science/Research




Categories

Bio-Informatics

This is an application that can also be fetched from https://sourceforge.net/projects/swiftseqaligner/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.


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