Tutorial

Install

git clone https://github.com/chenym1/IGTminer.git
cd IGTminer
IGTminer -h

Dependencies

IGTminer is implemented in python3 and CentOS Linux, and external command-line tools, which are executable on your PATH, are needed:
BLAST (v2.9.0)  The installing way: conda install blast -c bioconda
MCscan (v1.0.6)  The installing way: pip install jcvi
BEDTools (v2.29.2)  The installing way: conda install bedtools -c bioconda
R (v3.6.0)

Usages

IGTminer

$ IGTminer -h

Program:      IGTminer
Description:  A tool for nucleus organelle gene (NOG) map construction
Version:      v1.0.0

Usage:        IGTminer <command> [options]

Subcommands include:

[ pipeline ]
     reannotation          Reannotation of nucleus organelle genes (NOGs)
     collinearityNetwork   Pairwise collinear block search and construction of NOG map

reannotation - Reannotation of nucleus organelle genes

$ IGTminer reannotation -h

Tool:         IGTminer reannotation
Description:  Reannotation of nucleus organelle genes (NOGs)

Usage:        IGTminer reannotation [options]

Options:
  -h          Show this message and exit
  -g <file>   Gff3
  -f <file>   Nucleus genome fasta
  -c <file>   Chromosome name file
  -r <file>   Custom protein sequence file
  -m <str>    If parameter '-r' is empty, 
               please select plastid (pt) or mitochondrion (mt) [default pt]
  -p <file>   Organelle genome fasta
  -d <int>    Maximum distance for clustering NOGs [default 140000]
  -n <str>    Prefix name of output file [default NOG]
  -t <int>    Number of threads [default 12]

collinearityNetwork - Pairwise collinear block search and construction of NOG map

$ IGTminer collinearityNetwork -h

Tool:         IGTminer collinearityNetwork
Description:  Pairwise collinear block search and construction of NOG map

Usage:        IGTminer collinearityNetwork [options]

Options:
  -h          Show this message and exit
  -c <file>   Chromosome name path
  -n <file>   Prefix name of output file [default IGTminerOutput]
  -e          E-value of BLASTP [default 1e-5]
  -d <int>    Extent of flanking regions to search using MCscan [default 8]
  -s <int>    Minimum number of anchors in a cluster using MCscan [default 10]
  -t          Number of threads for blast [default 12]

Example

mkdir example; cd example
wget http://wheat.cau.edu.cn/TGT/downloads/example.tar.gz
tar -xzvf example.tar.gz
IGTminer reannotation -g te.gff3 -f te.fa -c te.chrlist -p te.pt.fa -n te
IGTminer reannotation -g svevo.gff3 -f svevo.fa -c svevo.chrlist -p svevo.pt.fa -n svevo
IGTminer collinearityNetwork -c chrlist