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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 <http://www.gnu.org/licenses/>. Contact the author by mkorpar@gmail.com. 1) DEPENDENCIES 2) INSTALLATION 3) USAGE :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 1) DEPENDENCIES :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: Application uses following software: 1) Linux shell 2) gcc 4.4 (for newest nvcc) - depends on nvcc version 3) nvcc 2.*+ 4) make :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 2) INSTALLATION :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: For installation run the install script in the application root directory from the command line. Application root directory must be writable. :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 3) USAGE :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: ./sw# -i <first_sequnce> -j <second_sequnce> [OPTIONS] [FLAGS] OPTIONS: --query, -i <first_sequnce> fasta query file path --target, -j <second_sequnce> fasta database file path fasta database are appended fasta files in a single text file --matrix-file <file_path> (optional) similarity matrix file path if given the similarity matrix is loaded from the file --matrix-table <BLOSUM50|BLOSUM55|BLOSUM62|BLOSUM70|DNA|BLAST|CHIAR> embedded similarity matrix (optional) (default: CHIAR) if given --matrix-file option won't be used --match <float> (optional) match value if --match and --mismatch are given, --matrix-table and --matrix-file options are not used --mismatch <float> (optional) mismacth value if --match and --mismatch are given, --matrix-table and --matrix-file options are not used --gap-open, -g <float> (optional) (default: 5.0) gap open value --gap-extend, -e <float> (optional) (default: 2.0) gap extend value --threshold <float> (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 --shotgun <int> (optional) (default: 0) - not used accepts a positive integer, target data is treated as blocks of given size separated with any character which is not a DNA symbol (A, C, T, G) --min-hits <int> (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 <int> (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
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CUDA parallelized version of Smith-Waterman algorithm
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