swift sequence alignment program

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.


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