https://github.com/solida-core/niasmic

Non Invasive Analysis of Somatic Mutations in Cancer
https://github.com/solida-core/niasmic

Last synced: 7 months ago
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Non Invasive Analysis of Somatic Mutations in Cancer

• Host: GitHub
• URL: https://github.com/solida-core/niasmic
• Owner: solida-core
• License: gpl-3.0
• Created: 2021-03-11T16:43:09.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2021-06-18T16:31:55.000Z (almost 5 years ago)
• Last Synced: 2024-12-27T20:46:12.958Z (over 1 year ago)
• Language: Python
• Size: 75.2 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
[![depends](https://img.shields.io/badge/depends%20from-bioconda-brightgreen.svg)](http://bioconda.github.io/)

[![snakemake](https://img.shields.io/badge/snakemake-5.3-brightgreen.svg)](https://snakemake.readthedocs.io/en/stable/)

[![Travis](https://travis-ci.com/solida-core/dima.svg?branch=master)](https://travis-ci.com/solida-core/dima.svg?branch=master)

# NIASMIC

**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.

All **[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.

Pipelines 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.

Software 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.

### Pipeline Handbook

**NIASMIC** pipeline documentation can be found in the `docs/` directory:

1. [Pipeline Structure:](https://github.com/solida-core/docs/blob/master/pipeline_structure.md)

    * [Snakefile](https://github.com/solida-core/docs/blob/master/pipeline_structure.md#snakefile)

    * [Configfile](https://github.com/solida-core/docs/blob/master/pipeline_structure.md#configfile)

    * [Rules](https://github.com/solida-core/docs/blob/master/pipeline_structure.md#rules)

    * [Envs](https://github.com/solida-core/docs/blob/master/pipeline_structure.md#envs)

2. [Pipeline Workflow](docs/dima_workflow.md)

3. [Required Files:]()

    * [Reference files](docs/reference_files.md)

    * [User files](docs/user_files.md)

4. [Running the pipeline:]()

    * [Manual Snakemake Usage](docs/dima_snakemake.md)

    * [SOLIDA:]()

        * [CLI - Command Line Interface](https://github.com/solida-core/solida/blob/master/README.md)

        * [GUI - Graphical User Interface]()

### Contact us

[support@solida-core](mailto:m.massidda@crs4.it)