https://github.com/brahle/swsharp

CUDA parallelized version of Smith-Waterman algorithm
https://github.com/brahle/swsharp

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CUDA parallelized version of Smith-Waterman algorithm

• Host: GitHub
• URL: https://github.com/brahle/swsharp
• Owner: brahle
• Created: 2011-10-20T14:23:35.000Z (about 13 years ago)
• Default Branch: master
• Last Pushed: 2011-10-16T14:07:46.000Z (about 13 years ago)
• Last Synced: 2023-03-11T12:17:51.328Z (over 1 year ago)
• Language: C
• Homepage:
• Size: 264 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README

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README

        
SW# - CUDA parallelized Smith Waterman with applying Hirschberg's algorithm

Copyright (C) 2011 Matija Korpar

This program is free software: you can redistribute it and/or modify

it under the terms of the GNU General Public License as published by

the Free Software Foundation, either version 3 of the License, or

(at your option) any later version.

This program is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

GNU General Public License for more details.

You should have received a copy of the GNU General Public License

along with this program.  If not, see .

Contact the author by [email protected].

1) DEPENDENCIES

2) INSTALLATION

3) USAGE

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1) DEPENDENCIES

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Application uses following software:

    1) Linux shell

    2) gcc 4.*+

    3) nvcc 2.*+

    4) make

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2) INSTALLATION

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For installation run the install script in the application root directory from

the command line. Application root directory must be writable.

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3) USAGE

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./sw# -i  -j  [OPTIONS] [FLAGS]

OPTIONS:

    --query, -i                                       

        fasta query file path

    --target, -j 

        fasta database file path

        fasta database are appended fasta files in a single text file

    --matrix-file  

        (optional)

        similarity matrix file path 

        if given the similarity matrix is loaded from the file

    --matrix-table 

        embedded similarity matrix

        (optional) 

        (default: CHIAR) 

        if given --matrix-file option won't be used

    --match  

        (optional)

        match value  

        if --match and --mismatch are given, --matrix-table and --matrix-file 

        options are not used

    --mismatch  

        (optional)

        mismacth value  

        if --match and --mismatch are given, --matrix-table and --matrix-file 

        options are not used

    --gap-open, -g  

        (optional)

        (default: 5.0)

        gap open value

    --gap-extend, -e  

        (optional)

        (default: 2.0)

        gap extend value  

    --threshold 

        (optional)

        (default: NO_THRESHOLD)

        score threshold

        program will output not just the max score and its reconstruction, but

        all the scores which are above the given threshold

    --min-hits 

        (optional)

        (default: 0)

        the option is used with --window option, it means there must be at 

        least min_hits of matchings in every window length segment

    --window 

        (optional)

        (default: 0)

        the option is used with --min-hits option, it means there must be at 

        least min_hits of matchings in every window length segment

FLAGS:

    --complement 

        (optional)

        if input is a nucleotide, search also the other strand 

    --solve 

        (optional)

        solve only 

    --cpu 

        (optional)

        force CPU solving

    --param-search 

        (optional)

        CUDA block and thread number optimization search

    --verbose

        (optional)

        verbose

    --global 

        (optional)

        global aligment 

        if given --threshold this option won't be used