{"id":33051378,"url":"https://github.com/hewm2008/NGenomeSyn","last_synced_at":"2025-11-18T21:01:06.471Z","repository":{"id":41565161,"uuid":"476207452","full_name":"hewm2008/NGenomeSyn","owner":"hewm2008","description":"Any Way to Show  Multi genomic Synteny ","archived":false,"fork":false,"pushed_at":"2025-07-04T05:30:20.000Z","size":19331,"stargazers_count":201,"open_issues_count":5,"forks_count":18,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-09-05T19:13:58.357Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/hewm2008.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2022-03-31T07:57:48.000Z","updated_at":"2025-07-23T09:39:08.000Z","dependencies_parsed_at":"2025-04-09T03:26:17.094Z","dependency_job_id":"d9b8b4eb-21e1-438e-b0ef-ed70d4c91aba","html_url":"https://github.com/hewm2008/NGenomeSyn","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"purl":"pkg:github/hewm2008/NGenomeSyn","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hewm2008%2FNGenomeSyn","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hewm2008%2FNGenomeSyn/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hewm2008%2FNGenomeSyn/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hewm2008%2FNGenomeSyn/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/hewm2008","download_url":"https://codeload.github.com/hewm2008/NGenomeSyn/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hewm2008%2FNGenomeSyn/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":285138471,"owners_count":27121052,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-11-18T02:00:05.759Z","response_time":61,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-11-14T03:00:27.111Z","updated_at":"2025-11-18T21:01:06.458Z","avatar_url":"https://github.com/hewm2008.png","language":"Perl","funding_links":[],"categories":["Comparative"],"sub_categories":[],"readme":"\n# NGenomeSyn\n\nAn easy-to-use and flexible tool for publication-ready visualization of syntenic relationships on multiple genomes\n\nThe \u003ci\u003e\u003cb\u003e[NGenomeSyn article](https://doi.org/10.1093/bioinformatics/btad121)\u003c/b\u003e\u003c/i\u003e has been published in \u003cb\u003e [Bioinformatics](https://doi.org/10.1093/bioinformatics/btad121) Journal\u003c/b\u003e, please cited this article if possible\n\nPMID: [36883694](https://pubmed.ncbi.nlm.nih.gov/36883694/)   \u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;            DOI:[10.1093/bioinformatics/btad121](https://doi.org/10.1093/bioinformatics/btad121)\n\n###  1 Introduction\n\u003cb\u003eNGenomeSyn\u003c/b\u003e, an easy-to-use and flexible tool, for publication-quality visualization of syntenic relationships (user-defined or generated by our custom script) and genomic features (e.g. repeats, structural variations, genes) on tens of genomes with high customization. NGenomeSyn allows its user to adjust default options for genome and link styles defined in the configuration file and simply adjusts options of moving, scaling, and rotation of target genomes, yielding a rich layout and publication-ready figure. A state-to-the-art figure enables users and readers to quickly catch key points hidden in the large-amount data at a galance. Moreover, NGenomeSyn could be applied on the visualization of relationships among other data with a similar input format (similar to sankey diagram).\n\nIn addition, \u003cb\u003eNGenomeSyn\u003c/b\u003e  has been cited to visualize genome synteny or other relationship by [Yin X et al 2022](https://www.sciencedirect.com/science/article/pii/S2590346222002590) ,  [X Hou et al 2022](https://doi.org/10.1016/j.molp.2022.05.014), [J Guan et al 2022](https://www.nature.com/articles/s41467-022-33515-2), [lian xu et 2022](https://www.nature.com/articles/s41597-022-01783-8), [G Cheng et al 2023](https://www.frontiersin.org/articles/10.3389/fpls.2023.1124046/full) ect\n\t  \n\n\u003c/br\u003eThe advantages of this tool include\n*\ttens of customizable genomes (\u003e=2)\n*\tflexible and customizable layout\n*\thigh customization for order, colors or other settings for each genome\n*\tallow setting for movement, rotation, scaling etc for each genome, which could generate particular layouts, such as triangle, quadrangle, pentagon etc\n*\thigh customization for color, transparency etc for link information\n\u003c/br\u003e\n\n\n###  2 Download and Install\n------------\nThe \u003cb\u003enew version\u003c/b\u003e will be updated and maintained in \u003cb\u003e[hewm2008/NGenomeSyn](https://github.com/hewm2008/NGenomeSyn)\u003c/b\u003e, please click below website to download the latest version\n\u003c/br\u003e\u003cp align=\"center\"\u003e\u003cb\u003e[hewm2008/NGenomeSyn](https://github.com/hewm2008/NGenomeSyn)\u003c/b\u003e\u003c/p\u003e\n\n\u003cb\u003elinux/MaxOS\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;  [Download](https://github.com/hewm2008/NGenomeSyn/archive/v1.43.tar.gz)\u003c/b\u003e\n\u003c/br\u003e\u003cb\u003eInstall\u003c/b\u003e\n\u003c/br\u003e \u003cb\u003e2.2 Pre-install\u003c/b\u003e\n\u003c/br\u003e The prerequisites for NGenomeSyn include\n\u003c/br\u003e 1) [Perl](https://www.perl.org/) with the [SVG.pm](https://metacpan.org/release/SVG) in Perl should be installed.(Note: SVG module is optional because related modules have been included in [bin/svg-kit]() directory)\n\u003c/br\u003e 2) [convert](https://linux.die.net/man/1/convert) is recommended to be pre-installed if requiered converting `svg` to `png` image format.\n\n\u003c/br\u003eUsers can install it with the following commands: \n\u003cpre\u003e\n        git clone https://github.com/hewm2008/NGenomeSyn.git\n        cd NGenomeSyn;\tchmod -R 755 bin/*\n        ./bin/NGenomeSyn  -h \n\u003c/pre\u003e\n\n\n###  3 Parameter description\n------------\n\u003c/br\u003e\u003cb\u003e3.1 NGenomeSyn\u003c/b\u003e\n\u003c/br\u003e\u003cb\u003e3.1.1 Main parameter\u003c/b\u003e\n\n```php\n        Usage: NGenomeSyn  -InConf  in.conf -OutPut OUT\n\n                -InConf      \u003cs\u003e : InPut Configuration File\n                -OutPut      \u003cs\u003e : OutPut svg file result\n\n                -help              See more help *Manual.pdf\n                                   [hewm2008 v1.43]\n\n```\n\u003c/br\u003eComments: we also provide a custom perl script [bin/GetTwoGenomeSyn.pl](https://github.com/hewm2008/NGenomeSyn/blob/main/bin/GetTwoGenomeSyn.pl) for link preparation information (see [exmaple1/run2.sh](https://github.com/hewm2008/NGenomeSyn/blob/main/Example/example1/run2.sh))\n\u003c/br\u003e\n\u003c/br\u003eSee more detailed usage  in the\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp; \u003cb\u003e[Chinese Documentation](https://github.com/hewm2008/NGenomeSyn/blob/main/NGenomeSyn_manual_Chinese.pdf)\u003c/b\u003e\n\u003c/br\u003eSee more detailed usage in the\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp; \u003cb\u003e[English Documentation](https://github.com/hewm2008/NGenomeSyn/blob/main/NGenomeSyn_manual_English.pdf)\u003c/b\u003e\n\u003c/br\u003eSee the \u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp; \u003cb\u003e[Example Directory](https://github.com/hewm2008/NGenomeSyn/tree/main/Example)\u003c/b\u003e \u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp; and for more details. such as : input file format.\n\n\n\u003c/br\u003e\u003cb\u003e3.1.2 Other parameters\u003c/b\u003e\n\n\n```php\n###  # Detailed parameters please see  at the  NGenomeSyn_manual_English.pdf \n\nSetParaFor = global\n########## global and required parameters ######\nGenomeInfoFile1=./RefA.len ### set path for Genome1, GenomeInfoFileX, X is the number of Genome\nGenomeInfoFile2=./RefB.len ### set path for Genome2, Format(chr start End ...)\n\nLinkFileRef1VsRef2=./RefA_RefB.link ### link information between Genome1 and Genome2\n                                    ### LinkFileRefXXVsRefYY : link info between GenomeXX and GenomeYY\n                                    ### Format (chrA StartA EndA chrB StartB EndB ...\n\n\n############ canvas and figure[optional] ######\n#body=1200                 ### size of canvas with width and height. plot region:  (up/down/left/right)=(55,25,100,120)\n#up=55\n#down=25\n#left=100\n#right=120\n#CanvasHeightRitao=1.0     ## adjust height of the plot\n#CanvasWidthRitao=1.0      ## adjust width of the plot\n#NoPng=1                   ## No OutPut the png File\n\n\n############# adjust genome setting [optional]##########\nSetParaFor = Genome1       ## GenomeALL/GenomeX\n#ZoomChr=1.0               ## adjust chr length, 1 for equal; \u003e1 for enlarge; \u003c1  for\n#RotateChr=30              ## rotate the chr with 30 degrees\n#ShiftX=0\n#ShiftY=0                  ## move the start of chr to (X,Y)\n#MoveToX                   ## MoveToY   ## similar to ShiftX and ShiftY\n\n\n#ChrWidth=20               ## chr width\n#LinkWidth=180             ## link height between this genome and next genome\n#ChrSpacing=10             ## spacing width of chr/scaffolds\n#NormalizedScale=0         ## custom scale for the geome relative the  default.\n#SpeRegionFile=Spe.bed     ## input file for highlighted regions[chr start end key1=value1] in the genome.\n#ZoomRegion                ## Zoom the specific Region,format (ZoomRegion=chr2:1000:5000)\n\n\n#GenomeNameRatio\n#GenomeName\n## GenomeName  GenomeNameSizeRatio  GenomeNameColor  GenomeNameShiftX GenomeNameShiftY\n## ChrNameShow ChrNameShiftX ChrNameShiftY ChrNameSizeRatio ChrNameColor ChrNameRotate\n## ShowCoordinates=1     ## Show Coordinates with other para [ScaleNum=10 ScaleUpDown ScaleUnit LabelUnit  LablefontsizeRatio  RotateAxisText NoShowLabel ]\n\n\nSetParaFor = Genome2       ##\n\n############# adjust link setting [optional]##########\nSetParaFor=Link1           ### LinkALL/LinkX  setting for link X\n#StyleUpDown=UpDown        ## UpDown DownUp UpUp DownDown line\n#Reverse=1                 ## reverse links\n#HeightRatio=1.0           ## ratio of link height relative to the default\n## other attributes:  fill|stroke|stroke-opacity|fill-opacity|stroke-width\n\n\n```\n\n\u003c/br\u003e\u003cb\u003e3.2 Output files\u003c/b\u003e\n\u003cpre\u003e\nout.svg: Output plot in SVG format\nout.png: Output plot in png format # convert should be installed\n\u003c/pre\u003e\n\n\n###  4 Examples\n------------\n\n\n\u003c/br\u003e ## directory  [[Example/example\\*/](https://github.com/hewm2008/NGenomeSyn/tree/main/Example)] has input and output file and script usage.\n\u003c/br\u003e\u003c/br\u003e\n\t\t../../bin/NGenomeSyn       -InConf        in.conf     -OutPut OUT\n\u003c/br\u003e\u003c/br\u003e \n\n|  \u003cb\u003eExample\u003c/b\u003e               |                                                 \u003cb\u003eDescription\u003c/b\u003e                                                |\n|-------------------------------|-------------------------------------------------------------------------------------------------------------------|\n|  \u003ci\u003e\u003cb\u003eexample1\u003c/b\u003e\u003c/i\u003e       |   An integrating \u003cb\u003epipeline\u003c/b\u003e including data preparation and visualizing of two genomes for the simplest usage        |\n|  \u003ci\u003e\u003cb\u003eexample2\u003c/b\u003e\u003c/i\u003e       |   Horizontal layout of 3 or more genomes,  genome layout adjustment and special region \u003cb\u003ehighlight\u003c/b\u003e           |\n|  \u003ci\u003e\u003cb\u003eexample3 \u003c/b\u003e\u003c/i\u003e      |  Link settings, five link styles, genome layout adjustment for particular shape (triangle)                        |\n|  \u003ci\u003e\u003cb\u003eexample4\u003c/b\u003e\u003c/i\u003e       |  \u003cb\u003eZoomRegion\u003c/b\u003e function of local \u003cb\u003egene structure\u003c/b\u003e(CDS mRNA) collinearity                                 |\n|  \u003ci\u003e\u003cb\u003eexample5\u003c/b\u003e\u003c/i\u003e       |  The comprehensive configuration for horizontal layout of more than three genomes (\u003e3)  |\n|  \u003ci\u003e\u003cb\u003eexample6\u003c/b\u003e\u003c/i\u003e       |  quick identification of genetic deletion in some breeds (pan-genome frequently analysis) to \u003cb\u003esolve biological issues\u003c/b\u003e problems |\n\n\u003c/br\u003e\n\n* Example 1)two genomes\n \u003c/br\u003eFor the simplest usage, only two genomic locus files and link file are required to be provided(Minimap2).\n  \u003c/br\u003ethe Minimap2 genome method\n![Minimap2.png](https://github.com/hewm2008/NGenomeSyn/blob/main/Example/example1/Minimap2.png)\n  \u003c/br\u003ethe MCScanX  gene method\n![MCScanX.png](https://github.com/hewm2008/NGenomeSyn/blob/main/Example/example1/MCScanX.png)\n  \u003c/br\u003eAlso the link file can be provided by [syri](https://schneebergerlab.github.io/syri/), see the run3.sh\n![Syri.png](https://github.com/hewm2008/NGenomeSyn/blob/main/Example/example1/Syri.png)\n\n* Example 2) Horizontal layout of 3 or more genomes\n\n![out.png](https://github.com/hewm2008/NGenomeSyn/blob/main/Example/example2/OUT1.png)\n\n* Example 2)Horizontal layout of 3 or more genomes with rotation of the third genome\n\n![out.png](https://github.com/hewm2008/NGenomeSyn/blob/main/Example/example2/OUT2.png)\n\n* Example 2)move the three genomes MoveX Y to the middle of the canvas, and rotate the genomes at -135, -45 and 90 degrees respectively. \n![out3.png](https://github.com/hewm2008/NGenomeSyn/blob/main/Example/example2/OUT3.png)\n\n\n* Example 3)any layout of three genomes for link setting\n\u003c/br\u003e trilateral layout :Five link styles were designed in this tools, \"DownDown\", \"UpUp\", \"DownUp\",\"UpDown\",\"line\".\n![out.png](https://github.com/hewm2008/NGenomeSyn/blob/main/Example/example3/OUT1.png)\n![out.png](https://github.com/hewm2008/NGenomeSyn/blob/main/Example/example3/OUT3.png)\n\n\n* Example 4) publication-ready and flexible layout for multiple genomes\n![out.png](https://github.com/hewm2008/NGenomeSyn/blob/main/Example/example4/OUT.png)\n\u003c/br\u003e we could generate a similar figure presented by [Zheng et al](https://onlinelibrary.wiley.com/doi/10.1111/jipb.13217) as follows\n![out.png](https://github.com/hewm2008/NGenomeSyn/blob/main/Example/example4/PMID34990066Fig2.png)\n\n* Example 5) local synteny in gene structure and ZoomRegion \n\u003c/br\u003ewe provide a parameter (SpeRegionWidthRatio) for controlling width of SpeRegion, supporting highlight gene structures (e.g. CDS, UTR etc)\n![out.png](https://github.com/hewm2008/NGenomeSyn/blob/main/Example/example5/OUT1.png)\n![out.png](https://github.com/hewm2008/NGenomeSyn/blob/main/Example/example5/OUT2.png)\n\n* Example 6) practical application (solve biological issues)\n\u003c/br\u003e In the pan-genome study, multiple genomes are de novo assembled from different individuals (accessions) independently, and it is often important to identify genetic structural variation (insertion and deletion) of different individuals (accessions) in a certain region to investigate whether link genetic variations to candidate genes that are responsible for important traits. The following example is an identification of some structural variations (insertion, deletion) in several rice accessions compared to the chromosome 12 of the reference rice genome (\"IRGSP\"). For example, a segment insertion occurs in the accessions of \"9311\" and \"ZH11\".\n![out.png](https://github.com/hewm2008/NGenomeSyn/blob/main/Example/example6/OUT.png)\n\n\u003c/br\u003e In fact, NGenomeSyn is not only designed for the visualization of genomic synteny and genomic features, but also for other relationships among any data with a similar input format. For example, a user ([lian xu et 2022](https://www.nature.com/articles/s41597-022-01783-8)) used NGenomeSyn for visualization clusters with similar gene expression patterns (generated by Mfuzz software) between other four datasets and the reference dataset and revealed conserved expression patterns of differential expression genes among different datasets.\n\n![realityData.png](https://github.com/hewm2008/NGenomeSyn/blob/main/Example/RealData/Other/realityData.png)\n\n### 5 Citation\n------------\nplease cited this [article](https://doi.org/10.1093/bioinformatics/btad121) if possible\n\u003c/br\u003eWeiming He, Jian Yang, Yi Jing, Lian Xu, Kang Yu, Xiaodong Fang, NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes, Bioinformatics, 2023;, btad121, https://doi.org/10.1093/bioinformatics/btad121\n\n### 6 Contact\n------------\n- [:email:](https://github.com/hewm2008/NGenomeSyn) hewm2008@gmail.com / hewm2008@qq.com\n- join the\u003cb\u003e\u003ci\u003e QQ Group : 125293663\u003c/b\u003e\u003c/i\u003e\n\n\n######################swimming in the sky and flying in the sea #############################\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhewm2008%2FNGenomeSyn","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhewm2008%2FNGenomeSyn","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhewm2008%2FNGenomeSyn/lists"}