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

Snakemake pipeline to map DNA datasets to a given reference genome using BWA MEM and Samtools.
https://github.com/solida-core/dima

bioinformatics genomics ngs-pipeline snakemake snakemake-workflows workflows

Last synced: 12 days ago
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Snakemake pipeline to map DNA datasets to a given reference genome using BWA MEM and Samtools.

• Host: GitHub
• URL: https://github.com/solida-core/dima
• Owner: solida-core
• License: gpl-3.0
• Created: 2019-01-14T09:27:22.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2022-07-15T12:42:28.000Z (over 2 years ago)
• Last Synced: 2023-10-20T23:11:33.919Z (about 1 year ago)
• Topics: bioinformatics, genomics, ngs-pipeline, snakemake, snakemake-workflows, workflows
• Language: Python
• Homepage:
• Size: 245 MB
• Stars: 1
• Watchers: 4
• Forks: 2
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Snakemake workflow: DiMA

[![Snakemake](https://img.shields.io/badge/snakemake-≥6.15.0-brightgreen.svg)](https://snakemake.bitbucket.io)

This workflow performs mapping of single-end and paired-end reads in fastq format against a reference genome to produce a deduplicated and recalibrated BAM file.

DiMA is part of the Snakemake-based pipelines collection [solida-core](https://github.com/solida-core) developed and manteined at [CRS4](https://www.crs4.it). 







## Authors

* Matteo Massidda (@massiddaMT)

* Rossano Atzeni (@ratzeni)

## Usage

The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog?usage=solida-core/dima).

If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and its DOI (see above).

## INSTRUCTIONS

Create a virtual environment with the command:

```commandline

mamba create -c bioconda -c conda-forge --name snakemake snakemake=6.15 snakedeploy

```

and activate it:

```commandline

conda activate snakemake

```

We get some public data to test the pipeline. You can directly clone in this folder from github, just type:

```commandline

git clone https://github.com/solida-core/test-data-DNA.git

```

You can then perform the pipeline deploy defining a directory `my_dest_dir` for analysis output and a pipeline tag for a specific version:

```bash

snakedeploy deploy-workflow https://github.com/solida-core/dima 

                    my_desd_dir 

```

To run the pipeline, go inside the deployed pipeline folder and use the command:

```bash

snakemake --use-conda -p --cores all

```

You can generate analysis report with the command:

```bash

snakemake --report report.zip --cores all

```