FGAP\u5229\u7528BLAST\u5c06contigs\u5e8f\u5217\u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4\u8349\u56fe\u5e8f\u5217\u4e0a\uff0c\u5bfb\u627e\u91cd\u53e0\u5230gap\u533a\u95f4\u7684\u6700\u4f18\u5e8f\u5217\uff0c\u4ece\u800c\u8fdb\u884c\u8865\u6d1e\u3002\u5176\u53c2\u8003\u6587\u732e\uff1aPiro, Vitor C., et al. “FGAP: an automated gap closing tool.” BMC research notes 7.1 (2014): 371.<\/a><\/p>\n FGAP\u5b98\u7f51\uff1ahttp:\/\/www.bioinfo.ufpr.br\/fgap\/<\/a>\u3002<\/p>\n FGAP\u7684\u7b80\u5355\u4f7f\u7528\u793a\u4f8b\uff1a<\/p>\n FGAP\u7684\u4f7f\u7528\u53c2\u6570\uff1a<\/p>\n 1. FGAP\u7b80\u4ecb FGAP\u5229\u7528BLAST\u5c06contigs\u5e8f\u5217\u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4\u8349\u56fe\u5e8f … \u7ee7\u7eed\u9605\u8bfb 2. FGAP\u4e0b\u8f7d\u548c\u5b89\u88c5<\/h1>\n
\r\n$ wget http:\/\/sourceforge.net\/projects\/fgap\/files\/MCR_LINUX64b.tar.gz\/download\r\n$ tar zxf MCR_LINUX64b.tar.gz\r\n$ cd MCR_LINUX64b\r\n$ .\/installMCR.sh \/opt\/biosoft\/MCR\r\n\r\n$ wget http:\/\/sourceforge.net\/projects\/fgap\/files\/FGAP_1_7_LINUX64b.tar.gz\/download\r\n$ tar zxf FGAP_1_7_LINUX64b.tar.gz -C \/opt\/biosoft\/\r\n<\/pre>\n
2. FGAP\u7684\u4f7f\u7528<\/h1>\n
\r\n$ ln -s \/opt\/biosoft\/FGAP_1_7_LINUX64b\/sample_data\/* .\r\n$ \/opt\/biosoft\/FGAP_1_7_LINUX64b\/run_fgap.sh \/opt\/biosoft\/MCR\/v717\/ \\\r\n -d DRAFT_ecoli_hiseq454.fasta \\\r\n -a \"DATASET_ecoli_454.fasta,DATASET_ecoli_hiseq.fasta\"\r\n<\/pre>\n
\r\n-d \/--draft-file\tDraft genome file [fasta format - Ex: \"draft.fasta\"]\r\n-a \/--datasets-files\tList of datasets files to close gaps [fasta format - Ex: \"dataset1.fasta,dataset2.fasta\"]\r\n\r\n-s \/--min-score\t\tMin Score (raw) to return results from BLAST (integer) - Default: 25\r\n-e \/--max-evalue\tMax E-Value to return results from BLAST (float) - Default: 1e-7\r\n-i \/--min-identity\tMin identity (%) to return results from BLAST (integer [0-100]) - Default: 70\r\n\r\n-C \/--contig-end-length\tLength (bp) of contig ends to perform BLAST alignment (integer) - Default: 300\r\n-T \/--edge-trim-length\tLength of ignored bases (bp) upstream and downstrem of the gap (integer) - Default: 0\r\n-R \/--max-remove-length\tMax number of bases (bp) that can be removed (integer) - Default: 500\r\n-I \/--max-insert-length\tMax number of bases (bp) that can be inserted (integer) - Default: 500\r\n\r\n-p \/--positive-gap\tEnable closing of positive gaps (with insertion) (integer [0-1]) - Default: 1\r\n-z \/--zero-gap\t\tEnable closing of zero gaps (without insert any base) (integer [0-1]) - Default: 0\r\n-g \/--negative-gap\tEnable closing of negative gaps (overlapping contig ends) (integer [0-1]) - Default: 0\r\n\r\n-c \/--gap-char\t\t\t\tBase that represents the gap (char) - Default: \"N\"\r\n-b \/--blast-path\t\t\tBlast+ package path (only makeblastdb and blastn are needed, version 2.2.28+ or higher) - Default: \"\"\r\n-l \/--blast-alignment-parameters\tBLAST alignment parameters (opengap,extendgap,match,mismatch,wordsize) - Default: \"1,1,1,-3,15\"\r\n-r \/--blast-max-results\t\t\tMax results from BLAST for each query (integer) - Default: 200\r\n-t \/--threads\t\t\t\tNumber of threads (integer) - Default: 1\r\n\r\n-m \/--more-output\tMore output files with gap regions after and before gap closing (integer [0-1]) - Default: 0\r\n-o \/--output-prefix\tOutput prefix [File or folder - Ex: \"out\" or \"out\/\" ] - Default: \"output_fgap\"\r\n-h \/--help\t\tThis help message\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"