About
Installation and usage of GenomeSyn is very easy. Users can download the GenomeSyn package from following ways:
Source code
GenomeSyn 1.2 is an OSI certified open source package. You can download the current source distribution or access Github.
Desktop
Simple click to download GenomeSyn package. This is an executable file, you can run it directly.
Install
- Simple click to GenomeSyn(Perl)/GenomeSyn(Python). They are executable files, you can run it directly.
- GenomeSyn is open source,so you can download the source code and modify the appropriate source code to suit their needs. (Perl/Python)
- If you use the GenomeSyn, you need to solve the software dependency problem first.
- You can download example data to test .
## GenoemSyn: A software for the visualization of genome synteny
GenomeSyn is an easy-to-use application, users only need to submit two or three genomes data of the same species and different species, GenomeSyn will automatically process these genomic data, which can realize the visualization from sequence alignment to genome synteny analysis the whole process of drawing out. To complete sequence alignment and genome synteny analysis visualization, GenomeSyn performs the following steps:
1. the user provides two to three FASTA file data of the same species genome, as well as optional additional data files in BED, GFF3 and other formats-genome annotation files.
2. When the user does not provide the coords file, GenomeSyn will call the comparison tool MUMmer to compare the submitted genome FASTA files, and generate the coords comparison file of the corresponding genome.
3. Perform genomic synteny analysis and visualization based on the files and parameters provided by the user. When the user provides the coords file or generates the coords file by calling the alignment tool, GenomeSyn will perform genome synteny analysis and visualization according to the files and parameters provided by the user.
GenomeSyn is very easy to download, install and use. Users can download and unzip the GenomeSyn package using wget or through git. After decompression, use the "source install.sh" command to add the environment for running GenomeSyn to run GenomeSyn. The steps for calling the comparison tool MUMmer are not included here, if users need to use the MUMmer comparison steps, they can install MUMmer by themselves through the following installation steps or install MUMmer through the setup_mummer.sh provided in the installation package. After MUMmer is successfully installed, you can use GenomeSyn's one-stop service.
```
# download the GenomeSyn with the link https://cbi.gxu.edu.cn/GenomeSyn//download/download_pl/
or
$ git clone git@github.com:JM-SONG/GenomeSyn.git
or
$ wget https://github.com/JM-SONG/GenomeSyn/archive/refs/heads/main.zip
```
```
# add the environment for running GenomeSyn
$ source ./install.sh
```
## Dependencies
***1. MUMmer***
You can find MUMmer. 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
$ cd mummer-4.0.0beta2
$ ./configure --prefix=`pwd`
$ make
# Add MUMmer tools to your PATH
$ export PATH=/your_path/GenomeSyn/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 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.
###Input files
We need to run GenomeSyn in the bin directory of the GenomeSyn package, and at least need to enter two genome sequence files. The genome sequence file should be a fasta file with the following format:
When running GenomeSyn, at least two genome sequence files are required.
Quick start
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