Swift Sequence Alignment Program download for Linux

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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SCREENSHOTS:


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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