We have hosted the application swift sequence alignment program in order to run this application in our online workstations with Wine or directly.


Quick description about swift sequence alignment program:

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 [email protected].

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

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