{"id":33051394,"url":"https://github.com/martinghunt/ziplign","last_synced_at":"2026-03-09T15:33:34.951Z","repository":{"id":261120352,"uuid":"812924861","full_name":"martinghunt/ziplign","owner":"martinghunt","description":"Simple-to-use interactive comparison of two bacterial genomes","archived":false,"fork":false,"pushed_at":"2026-01-30T19:00:18.000Z","size":21173,"stargazers_count":19,"open_issues_count":18,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2026-01-31T11:50:41.708Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://ziplign.readthedocs.io/en/","language":"GDScript","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/martinghunt.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-06-10T07:01:58.000Z","updated_at":"2026-01-30T19:00:23.000Z","dependencies_parsed_at":"2024-11-27T09:23:04.843Z","dependency_job_id":"6ee47073-d36c-476d-ba61-4459fb8b5b46","html_url":"https://github.com/martinghunt/ziplign","commit_stats":null,"previous_names":["martinghunt/tna","martinghunt/ziplign"],"tags_count":6,"template":false,"template_full_name":null,"purl":"pkg:github/martinghunt/ziplign","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/martinghunt%2Fziplign","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/martinghunt%2Fziplign/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/martinghunt%2Fziplign/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/martinghunt%2Fziplign/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/martinghunt","download_url":"https://codeload.github.com/martinghunt/ziplign/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/martinghunt%2Fziplign/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30301109,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-09T14:33:48.460Z","status":"ssl_error","status_checked_at":"2026-03-09T14:33:48.027Z","response_time":61,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":"2025-11-14T03:00:27.112Z","updated_at":"2026-03-09T15:33:34.937Z","avatar_url":"https://github.com/martinghunt.png","language":"GDScript","funding_links":[],"categories":["Comparative"],"sub_categories":[],"readme":"# Ziplign\n\n[![status](https://joss.theoj.org/papers/0fc2ce726ea149065995d899c9dc2f68/status.svg)](https://joss.theoj.org/papers/0fc2ce726ea149065995d899c9dc2f68)\n\nZiplign is a free application to visualise the comparison of two bacterial genomes.\nIt is intended to be easy to use: you just need to drag and drop two sequence\nfiles to compare. Ziplign will run BLAST for you and show you the results.\nThere is no need to use a terminal or type any commands.\n\nDocumentation: https://ziplign.readthedocs.io/en/\n\nCitation: Hunt et al., (2025). Ziplign: a simple-to-use interactive tool to compare bacterial genomes. Journal of Open Source Software, 10(116), 9004, https://doi.org/10.21105/joss.09004\n\n\u003cimg src=\"docs/pics/zl_docs_overview_screenshots.gif\" alt=\"demo screenshots\" width=\"80%\"\u003e\n\n## Quick start\n\n\n### Download Ziplign\n\nDownload the [latest release](https://github.com/martinghunt/ziplign/releases/latest)\nfor your operating system. It is available for Linux, Mac, and Windows 11.\nIf you are using Linux, then make the downloaded file\nexecutable (eg `chmod 755`).\n\nDouble-click the downloaded file to run Ziplign.\nThe first time Ziplign is run, it will download some extra programs such\nas BLAST. This might take some time depending on internet speed.\n\n\n\n### Test data\n\nCheck if the install is OK using the test data.\n\n1. Press the \"New\" button - this is the screen for loading new genomes.\n2. Press the icon with a tick at the top right,\nwhich will fill in the boxes to use the\nbuilt in test data. There is a screenshot in the\n[test data](https://ziplign.readthedocs.io/en/stable/installation.html#use-the-test-data)\ndocumentation.\n3. Press the \"Start\" button at the bottom. This will process the\ntest data and then switch to viewing the two genomes.\n\nYou should now be able to move around and zoom using the buttons near the top\nleft and/or the cursor keyboard keys. Zoom using the mouse wheel,\nor pinch gesture on a trackpad.\n\n\n### Real data\n\nGet back to the main menu using the back arrow at the top left, or by pressing\n\"q\".\n\n1. Press the \"New\" button again.\n2. To compare two genomes that are in files on your computer, drag and drop\none file into the \"Top genome file\" box, and\na second genome into the \"Bottom genome file\" box.\n3. Press the \"Start\" button at the bottom. Ziplign will run BLAST between the genomes and then\nswitch to viewing them.\n\nAlternatively, genome accessions can be used instead of files on your\ncomputer, and Ziplign will download the genomes from the NCBI.\nAs described in more detail in the [sequence files](https://ziplign.readthedocs.io/en/stable/loading.html#sequence-files)\ndocumentation, most common accession formats can be used, such as `GCA_*`, `NC_*` etc.\nFor example, the S. flexneri and E. coli K12 genomes `GCF_000007405.1` and\n`GCF_000005845.2`.\n\n\n### Further reading\n\nPlease see the full documentation at: https://ziplign.readthedocs.io/en/.\n\nHighlights of Ziplign include:\n* [Search](https://ziplign.readthedocs.io/en/stable/searching.html) for sequence\nor annotation features\n* [Basic editing](https://ziplign.readthedocs.io/en/stable/contig_editing.html).\nContigs can be reordered and reverse-complemented.\n* [Save/Load](https://ziplign.readthedocs.io/en/stable/saving_n_loading.html)\na project in a single file that stores both genomes and BLAST results.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmartinghunt%2Fziplign","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmartinghunt%2Fziplign","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmartinghunt%2Fziplign/lists"}