{"id":18676541,"url":"https://github.com/solida-core/diva.wgs","last_synced_at":"2025-11-07T06:30:34.863Z","repository":{"id":114069330,"uuid":"171894704","full_name":"solida-core/diva.wgs","owner":"solida-core","description":null,"archived":false,"fork":false,"pushed_at":"2021-01-29T08:01:33.000Z","size":78,"stargazers_count":0,"open_issues_count":1,"forks_count":3,"subscribers_count":1,"default_branch":"master","last_synced_at":"2024-12-27T20:46:12.672Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/solida-core.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}},"created_at":"2019-02-21T15:16:08.000Z","updated_at":"2021-01-29T08:01:36.000Z","dependencies_parsed_at":null,"dependency_job_id":"39ef4f51-a794-4198-b392-56fb3eb7b9fc","html_url":"https://github.com/solida-core/diva.wgs","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/solida-core%2Fdiva.wgs","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/solida-core%2Fdiva.wgs/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/solida-core%2Fdiva.wgs/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/solida-core%2Fdiva.wgs/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/solida-core","download_url":"https://codeload.github.com/solida-core/diva.wgs/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239520734,"owners_count":19652747,"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":[],"created_at":"2024-11-07T09:29:38.478Z","updated_at":"2025-11-07T06:30:34.818Z","avatar_url":"https://github.com/solida-core.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![depends](https://img.shields.io/badge/depends%20from-bioconda-brightgreen.svg)](http://bioconda.github.io/)\n[![snakemake](https://img.shields.io/badge/snakemake-5.3-brightgreen.svg)](https://snakemake.readthedocs.io/en/stable/)\n[![Build Status](https://travis-ci.com/solida-core/diva.wgs.svg?branch=master)](https://travis-ci.com/solida-core/diva.wgs)\n# DiVA WGS\n**DiVA WGS** is a pipeline for Next-Generation Sequencing **Whole Genome** data anlysis.\n\nAll **[solida-core](https://github.com/solida-core)** workflows follow GATK Best Practices for Germline Variant Discovery, with the incorporation of further improvements and refinements after their testing with real data in various [CRS4 Next Generation Sequencing Core Facility](http://next.crs4.it) research sequencing projects.\n\nPipelines are based on [Snakemake](https://snakemake.readthedocs.io/en/stable/), a workflow management system that provides all the features needed to create reproducible and scalable data analyses.\n\nSoftware dependencies are specified into the `environment.yaml` file and directly managed by Snakemake using [Conda](https://docs.conda.io/en/latest/miniconda.html), ensuring the reproducibility of the workflow on a great number of different computing environments such as workstations, clusters and cloud environments.\n\n\n### Pipeline Overview\nThe pipeline workflow is composed by two major analysis sections:\n * [_Mapping_](docs/diva_workflow.md#mapping): single and/or paired-end reads in fastq format are aligned against a reference genome to produce a deduplicated and recalibrated BAM file. This section is executed by DiMA pipeline.\n\n * [_Variant Calling_](docs/diva_workflow.md#variant-calling): a joint call is performed from all project's bam files\n \nParallely, statistics collected during these steps are used to generate reports for [Quality Control](docs/diva_workflow.md#quality-control).\n\nA complete view of the analysis workflow is provided by the pipeline's [graph](images/diva-wgs.png).\n\n\n\n### Pipeline Handbook\n**DiVA WGS** pipeline documentation can be found in the `docs/` directory:\n\n\n1. [Pipeline Structure:](https://github.com/solida-core/docs/blob/master/pages/handbook/pipeline_struct.md)\n    * [Snakefile](https://github.com/solida-core/docs/blob/master/pages/handbook/pipeline_struct.md#snakefile)\n    * [Configfile](https://github.com/solida-core/docs/blob/master/pages/handbook/pipeline_struct.md#configfile)\n    * [Rules](https://github.com/solida-core/docs/blob/master/pages/handbook/pipeline_struct.md#rules)\n    * [Envs](https://github.com/solida-core/docs/blob/master/pages/handbook/pipeline_struct.md#envs)\n2. [Pipeline Workflow](docs/diva_workflow.md)\n3. Required Files:\n    * [Reference files](docs/reference_files.md)\n    * [User files](docs/user_files.md)\n4. Running the pipeline:\n    * [Manual Snakemake Usage](docs/diva_snakemake.md)\n    * SOLIDA:\n        * [CLI - Command Line Interface](https://github.com/solida-core/docs/blob/master/pages/solida/solida_cli.md)\n        * [GUI - Graphical User Interface](https://github.com/solida-core/docs/blob/master/pages/solida/solida_gui.md)\n\n\n\n\n\n\n### Contact us\n[support@solida-core](mailto:m.massidda@crs4.it) \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsolida-core%2Fdiva.wgs","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsolida-core%2Fdiva.wgs","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsolida-core%2Fdiva.wgs/lists"}