{"id":18619859,"url":"https://github.com/edinburgh-genome-foundry/primavera","last_synced_at":"2025-09-05T13:38:34.606Z","repository":{"id":62578059,"uuid":"109323765","full_name":"Edinburgh-Genome-Foundry/Primavera","owner":"Edinburgh-Genome-Foundry","description":":cherry_blossom: Python library for primer-based verification of DNA assemblies: primer selection, data analyis, etc.","archived":false,"fork":false,"pushed_at":"2025-04-09T15:03:50.000Z","size":2726,"stargazers_count":33,"open_issues_count":0,"forks_count":4,"subscribers_count":9,"default_branch":"master","last_synced_at":"2025-04-09T15:07:07.613Z","etag":null,"topics":["dna-assembly","primer-design","sequencing","synthetic-biology"],"latest_commit_sha":null,"homepage":"https://edinburgh-genome-foundry.github.io/Primavera/","language":"Python","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/Edinburgh-Genome-Foundry.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2017-11-02T22:06:34.000Z","updated_at":"2025-04-09T15:03:47.000Z","dependencies_parsed_at":"2022-11-03T19:39:10.391Z","dependency_job_id":null,"html_url":"https://github.com/Edinburgh-Genome-Foundry/Primavera","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Edinburgh-Genome-Foundry%2FPrimavera","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Edinburgh-Genome-Foundry%2FPrimavera/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Edinburgh-Genome-Foundry%2FPrimavera/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Edinburgh-Genome-Foundry%2FPrimavera/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Edinburgh-Genome-Foundry","download_url":"https://codeload.github.com/Edinburgh-Genome-Foundry/Primavera/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248329523,"owners_count":21085549,"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","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":["dna-assembly","primer-design","sequencing","synthetic-biology"],"created_at":"2024-11-07T04:03:35.851Z","updated_at":"2025-04-11T02:30:53.151Z","avatar_url":"https://github.com/Edinburgh-Genome-Foundry.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":".. raw:: html\n\n    \u003cp align=\"center\"\u003e\n    \u003cimg alt=\"Primavera Logo\" title=\"Primavera Logo\" src=\"https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Primavera/master/docs/_static/images/title.png\" width=\"550\"\u003e\n    \u003cbr /\u003e\u003cbr /\u003e\n    \u003c/p\u003e\n\n.. image:: https://github.com/Edinburgh-Genome-Foundry/Primavera/actions/workflows/build.yml/badge.svg\n    :target: https://github.com/Edinburgh-Genome-Foundry/Primavera/actions/workflows/build.yml\n    :alt: GitHub CI build status\n\n.. image:: https://coveralls.io/repos/github/Edinburgh-Genome-Foundry/Primavera/badge.svg?branch=master\n   :target: https://coveralls.io/github/Edinburgh-Genome-Foundry/Primavera?branch=master\n\n\n\nPrimavera is a Python library to plan and analyze primer-based verification of DNA assemblies, using Sanger sequencing or verification PCR. It implements methods to design and select primers to ensure that the relevant assembly segments will be covered, and can generate simple (but approximative) plots summarizing the results of a batch of Sanger sequencing.\n\nYou can see a live-demo for primer selection `on EGF CUBA: Select Primers \u003chttp://cuba.genomefoundry.org/select_primers\u003e`_.\n\nDocumentation: `API reference \u003chttps://edinburgh-genome-foundry.github.io/Primavera/\u003e`_\n\n\nUsage\n-----\n\n**Primer selection**\n\nThe following code assumes that a file ``available_primers.fa`` contains the labels and sequences of all available primers in the lab, and that the assemblies to be sequence-verified have annotations indicating the zones that the sequencing should cover and zones where primer annealing should be avoided.\n\n.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Primavera/master/docs/_static/images/annotated_genbank.png\n   :width: 600px\n\n.. code:: python\n\n    from primavera import PrimerSelector, Primer, load_record\n    import os\n\n    # LOAD ASSEMBLIES RECORDS AND AVAILABLE PRIMERS\n    records = [load_record(file_path, linear=False)\n               for file_path in ['my_record_1.gb', 'my_record_2.gb']]  # etc\n    available_primers = Primer.list_from_fasta('example_primers.fa')\n\n    # SELECT THE BEST PRIMERS\n    selector = PrimerSelector(tm_range=(55, 70), size_range=(16, 25))\n    selected_primers = selector.select_primers(records, available_primers)\n\n    # PLOT THE COVERAGE AND WRITE THE PRIMERS IN A SPREADSHEET\n    selector.plot_coverage(records, selected_primers, 'coverage.pdf')\n    selector.write_primers_table(selected_primers, 'selected_primers.csv')\n\nThe returned ``selected_primers`` contains a list of lists of primers (one list for each construct). The PDF report returned looks like this:\n\n.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Primavera/master/docs/_static/images/annotated_primer_selection.png\n   :width: 600px\n\n\nInstallation\n------------\n\nYou can install Primavera through PIP:\n\n.. code::\n\n    pip install primavera\n\nYou will also need to install the NCBI-BLAST+ software. For instance on Ubuntu:\n\n.. code:: shell\n\n    apt-get install ncbi-blast+\n\n\nLicense = MIT\n-------------\n\nPrimavera is an open-source software originally written at the `Edinburgh Genome Foundry \u003chttp://edinburgh-genome-foundry.github.io/home.html\u003e`_ by `Zulko \u003chttps://github.com/Zulko\u003e`_ and `released on Github \u003chttps://github.com/Edinburgh-Genome-Foundry/Primavera\u003e`_ under the MIT licence (Copyright 2017 Edinburgh Genome Foundry, University of Edinburgh). Everyone is welcome to contribute!\n\nMore biology software\n---------------------\n\n.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Edinburgh-Genome-Foundry.github.io/master/static/imgs/logos/egf-codon-horizontal.png\n :target: https://edinburgh-genome-foundry.github.io/\n\nPrimavera is part of the `EGF Codons \u003chttps://edinburgh-genome-foundry.github.io/\u003e`_ synthetic biology software suite for DNA design, manufacturing and validation.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fedinburgh-genome-foundry%2Fprimavera","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fedinburgh-genome-foundry%2Fprimavera","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fedinburgh-genome-foundry%2Fprimavera/lists"}