{"id":18676540,"url":"https://github.com/solida-core/niasmic","last_synced_at":"2025-11-07T06:30:34.767Z","repository":{"id":114067817,"uuid":"346770525","full_name":"solida-core/niasmic","owner":"solida-core","description":"Non Invasive Analysis of Somatic Mutations in Cancer","archived":false,"fork":false,"pushed_at":"2021-06-18T16:31:55.000Z","size":77,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2024-12-27T20:46:12.958Z","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":"2021-03-11T16:43:09.000Z","updated_at":"2021-06-18T16:31:57.000Z","dependencies_parsed_at":null,"dependency_job_id":"59f7bb07-7865-4537-8075-b8cdcc38ce06","html_url":"https://github.com/solida-core/niasmic","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%2Fniasmic","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/solida-core%2Fniasmic/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/solida-core%2Fniasmic/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/solida-core%2Fniasmic/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/solida-core","download_url":"https://codeload.github.com/solida-core/niasmic/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":"2024-11-07T09:29:38.350Z","updated_at":"2025-11-07T06:30:34.724Z","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[![Travis](https://travis-ci.com/solida-core/dima.svg?branch=master)](https://travis-ci.com/solida-core/dima.svg?branch=master)\n\n# NIASMIC\n**NIASMIC** (Non Invasive Analysis of Somatic Mutations in Cancer) is a pipeline for Next-Generation Sequencing data analysis for identification of somatic mutations in tumoral and ctDNA.\n\nAll **[solida-core](https://github.com/solida-core)** workflows follow GATK Best Practices for Germline and Somatic 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\n### Pipeline Handbook\n**NIASMIC** pipeline documentation can be found in the `docs/` directory:\n\n\n1. [Pipeline Structure:](https://github.com/solida-core/docs/blob/master/pipeline_structure.md)\n    * [Snakefile](https://github.com/solida-core/docs/blob/master/pipeline_structure.md#snakefile)\n    * [Configfile](https://github.com/solida-core/docs/blob/master/pipeline_structure.md#configfile)\n    * [Rules](https://github.com/solida-core/docs/blob/master/pipeline_structure.md#rules)\n    * [Envs](https://github.com/solida-core/docs/blob/master/pipeline_structure.md#envs)\n2. [Pipeline Workflow](docs/dima_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/dima_snakemake.md)\n    * [SOLIDA:]()\n        * [CLI - Command Line Interface](https://github.com/solida-core/solida/blob/master/README.md)\n        * [GUI - Graphical User Interface]()\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%2Fniasmic","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsolida-core%2Fniasmic","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsolida-core%2Fniasmic/lists"}