使用FGAP进行补洞

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

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