plotDotplot

The kit was used for displaying dotplot of genome alignment basing on mscan and mummer

Copyright (C) 2014 Arthur Zwaenepoel Apache License Version 2.0, January 2004 http://www.apache.org/licenses/

Beijing Genomics Institute, Animal and Plant research: https://www.genomics.cn/

#The Kit was used for displaying genomic collinearity basing on result of Mummer or Mscan.

Installation

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The Kit was writted mainly by perl, and tested with perl v5.10.1 on CentOS release 6.9. Install it, just simply execute as following.Then you can run it directly.

git clone  https://github.com/chenjunhui/plotDotplot/edit/plotDotplot

Notably, the kit depend on SVG package of perl, thus, you should install it and export PERL5LIB="/user/packages:$PERL5LIB" before run it.

Usage

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On the command line, just run

perl ../displayCollinearity.pl test0.syn  Actinidia_chinensis.Red5.len   kiwifruit.chr.len   colors.txt   test.svg --spec1 specie --spec2 specie --r 2 --unit 20  --identity 1

<br/> Input file

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• genome Length

LG1     21084470
LG10    22486653
LG11    16130964

• collinearity blocks

LG1     LG1     8087    9743    LG11    LG11    9655989 9657635 93.94
Specie1_chromosome   flag[chr|geneID]  start end   Specie2_chromosome   flag[chr|geneID]  start end   score

Parameters

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perl displayCollinearity.pl <syn_chr_file> <chr1_file> <chr2_file> <svg_out> [options]

 <blockFile>:   The synteny relationshiop or aligment between two genome.
 <queryLength>:  The species chromosomes length file plot in the X axis.
 <referenceLength>:The species chromosomes length file plot in the Y axis.
 <svg_out>:      The output svg file.
 --identity      Add identity to the figure if display the alignment.  [default: 0]
 --spec1 <str>:  Set the X axis title. [default:species1]
 --spec2 <str>:  Set the Y axis title. [default:species2]
 --r     <int>:  Set the radius of each syntenic dot. [default:3]
 --unit  <int>:  Set the scale on the X/Y axis. [default:20]
 --rx    <int>:  Set the resolution of X axis. [default:200000]
 --ry    <int>:  Set the resolution of Y axis. [default:200000]
 --reorder:      reorder chromosome of x axis basing on chromosome on y axis.
 --orderaxis:    axis needed to be ordered, default: x.
 --png:          Convert the svg file into png format.
 

Contributors

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chenjhbio: chenjunhui@genomics.cn