1. FGAP简介
FGAP利用BLAST将contigs序列比对到基因组草图序列上，寻找重叠到gap区间的最优序列，从而进行补洞。其参考文献：Piro, Vitor C., et al. “FGAP: an automated gap closing tool.” BMC research notes 7.1 (2014): 371.
2. FGAP下载和安装
FGAP官网：http://www.bioinfo.ufpr.br/fgap/。
$ wget http://sourceforge.net/projects/fgap/files/MCR_LINUX64b.tar.gz/download $ tar zxf MCR_LINUX64b.tar.gz $ cd MCR_LINUX64b $ ./installMCR.sh /opt/biosoft/MCR $ wget http://sourceforge.net/projects/fgap/files/FGAP_1_7_LINUX64b.tar.gz/download $ tar zxf FGAP_1_7_LINUX64b.tar.gz -C /opt/biosoft/
2. FGAP的使用
FGAP的简单使用示例：
$ ln -s /opt/biosoft/FGAP_1_7_LINUX64b/sample_data/* . $ /opt/biosoft/FGAP_1_7_LINUX64b/run_fgap.sh /opt/biosoft/MCR/v717/ \ -d DRAFT_ecoli_hiseq454.fasta \ -a "DATASET_ecoli_454.fasta,DATASET_ecoli_hiseq.fasta" FGAP的使用参数： -d /--draft-file Draft genome file [fasta format - Ex: "draft.fasta"] -a /--datasets-files List of datasets files to close gaps [fasta format - Ex: "dataset1.fasta,dataset2.fasta"] -s /--min-score Min Score (raw) to return results from BLAST (integer) - Default: 25 -e /--max-evalue Max E-Value to return results from BLAST (float) - Default: 1e-7 -i /--min-identity Min identity (%) to return results from BLAST (integer [0-100]) - Default: 70 -C /--contig-end-length Length (bp) of contig ends to perform BLAST alignment (integer) - Default: 300 -T /--edge-trim-length Length of ignored bases (bp) upstream and downstrem of the gap (integer) - Default: 0 -R /--max-remove-length Max number of bases (bp) that can be removed (integer) - Default: 500 -I /--max-insert-length Max number of bases (bp) that can be inserted (integer) - Default: 500 -p /--positive-gap Enable closing of positive gaps (with insertion) (integer [0-1]) - Default: 1 -z /--zero-gap Enable closing of zero gaps (without insert any base) (integer [0-1]) - Default: 0 -g /--negative-gap Enable closing of negative gaps (overlapping contig ends) (integer [0-1]) - Default: 0 -c /--gap-char Base that represents the gap (char) - Default: "N" -b /--blast-path Blast+ package path (only makeblastdb and blastn are needed, version 2.2.28+ or higher) - Default: "" -l /--blast-alignment-parameters BLAST alignment parameters (opengap,extendgap,match,mismatch,wordsize) - Default: "1,1,1,-3,15" -r /--blast-max-results Max results from BLAST for each query (integer) - Default: 200 -t /--threads Number of threads (integer) - Default: 1 -m /--more-output More output files with gap regions after and before gap closing (integer [0-1]) - Default: 0 -o /--output-prefix Output prefix [File or folder - Ex: "out" or "out/" ] - Default: "output_fgap" -h /--help This help message
原文来自:http://www.chenlianfu.com/?p=2333