We developed GenomeSyn as a new tool for constructing and visualizing genome synteny, its novel design and implementation can serve as a necessary complement to the study of genomic synteny and structural variation and its visualization tools.
An online service of GenomeSyn at: http://cbi.gxu.edu.cn/GenomeSyn/.
GenomeSyn is an executable file written in Perl, and users can run it directly. But before using GenomeSyn, the software dependency problem needs to be solved first. Users can download sample data for testing. GenomeSyn 1.2 is an OSI certified open source package. You can download the current source distribution here or access Github.
git clone git@github.com:JM-SONG/GenomeSyn.git
1. MUMmer
You can find MUMmer here. We used Mummer-4.0.0beta2. Mummer version 4.x.x requires a recent version of the GCC compiler (g++ version >= 4.7), which is hard to install if you have no administrator authority. You can ask your system administrator for some help in this case.
$ wget https://github.com/mummer4/mummer/releases/download/v4.0.0beta2/mummer-4.0.0beta2.tar.gz
$ tar -xvzf mummer-4.0.0beta2.tar.gz
$ current_path='pwd'
$ cd mummer-4.0.0beta2
$ ./configure --prefix=`pwd`
$ make
# Add MUMmer tools to your PATH
$ export PATH=$current_path/mummer-4.0.0beta2:$PATH
2. Perl and perl module
3. Python and python module
We have integrated the required Perl (localperl) and SVG and BioPerl package and Python (miniconda) and svglib packages in the GenomeSyn installation package, after the GenomeSyn installation package is decompressed, use the "source ./install.sh" command to add the environment for running GenomeSyn to run GenomeSyn.
# add the environment variables
$ source ./install.sh
eg. GenomeSyn -g1 ../data/rice_MH63.fa -g2 ../data/rice_ZS97.fa
eg. GenomeSyn -t 3 -g1 ../data/rice_MH63.fa -g2 ../data/rice_ZS97.fa -cf1 ../data/rice_MH63vsZS97.delta.filter.coords
eg. GenomeSyn -t 3 -g1 ../data/rice_MH63.fa -g2 ../data/rice_ZS97.fa -cf1 ../data/rice_MH63vsZS97.delta.filter.coords -cen1 ../data/rice_MH63_centromere.bed -cen2 ../data/rice_ZS97_centromere.bed -tel1 ../data/rice_MH63_telomere.bed -tel2 ../data/rice_ZS97_telomere.bed -TE1 ../data/rice_MH63_repeat.bed -TE2 ../data/rice_ZS97_repeat.bed -PAV1 ../data/rice_MH63_PAV.bed -PAV2 ../data/rice_ZS97_PAV.bed -NLR1 ../data/rice_MH63_NLR.bed -NLR2 ../data/rice_ZS97_NLR.bed -r MH63 -q ZS97 -GD1 ../data/rice_MH63_nonTEgene.gff3 -GD2 ../data/rice_ZS97_nonTEgene.gff3 -GC1 ../data/rice_MH63_GC_10000.bed -GC2 ../data/rice_ZS97_GC_10000.bed -GC_win 100000 -TE_min 40
eg. GenomeSyn -t 3 -n3 12 -g1 ../data/rice_MH63.fa -g2 ../data/rice_ZS97.fa -g3 ../data/rice_R498.fasta -cf1 ../data/rice_MH63vsZS97.delta.filter.coords -cf2 ../data/rice_MH63vsR498.delta.filter.coords -cen1 ../data/rice_MH63_centromere.bed -cen2 ../data/rice_ZS97_centromere.bed -cen3 ../data/rice_R498_centromere.bed -tel1 ../data/rice_MH63_telomere.bed -tel2 ../data/rice_ZS97_telomere.bed -tel3 ../data/rice_R498_telomere.bed -TE2 ../data/rice_ZS97_repeat.bed -PAV1 ../data/rice_MH63_PAV.bed -PAV2 ../data/rice_ZS97_PAV.bed -NLR1 ../data/rice_MH63_NLR.bed -NLR2 ../data/rice_ZS97_NLR.bed -r MH63 -q1 ZS97 -q2 R498 -GD1 ../data/rice_MH63_nonTEgene.gff3 -GD2 ../data/rice_ZS97_nonTEgene.gff3 -GD3 ../data/rice_R498_IGDBv3_coreset.gff -GC2 ../data/rice_ZS97_GC_10000.bed -GC_win 100000 -TE_min 40