https://github.com/dlaehnemann/create-ecdna-testing-data

A Snakemake workflow for creating testing data for ecDNA analysis workflows: long reads (Nanopore with NanoSim) and short reads (Illumina with seqkit and mason).
https://github.com/dlaehnemann/create-ecdna-testing-data

circular-dna ecdna illumina-sequencing nanopore-reads simulation snakemake workflow

Last synced: about 1 year ago
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A Snakemake workflow for creating testing data for ecDNA analysis workflows: long reads (Nanopore with NanoSim) and short reads (Illumina with seqkit and mason).

• Host: GitHub
• URL: https://github.com/dlaehnemann/create-ecdna-testing-data
• Owner: dlaehnemann
• License: mit
• Created: 2024-08-23T14:26:19.000Z (almost 2 years ago)
• Default Branch: main
• Last Pushed: 2025-02-12T15:52:22.000Z (over 1 year ago)
• Last Synced: 2025-02-12T16:46:08.177Z (over 1 year ago)
• Topics: circular-dna, ecdna, illumina-sequencing, nanopore-reads, simulation, snakemake, workflow
• Language: Python
• Homepage: https://snakemake.github.io/snakemake-workflow-catalog/?usage=dlaehnemann%2Fcreate-ecdna-testing-data
• Size: 43 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE

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README

          
# Snakemake workflow: `create-ecdna-testing-data`

[![Snakemake](https://img.shields.io/badge/snakemake-≥6.3.0-brightgreen.svg)](https://snakemake.github.io)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14814803.svg)](https://doi.org/10.5281/zenodo.14814803)

[![CI Tests](https://github.com/dlaehnemann/create-ecdna-testing-data/actions/workflows/main.yml/badge.svg?branch=main)](https://github.com/dlaehnemann/create-ecdna-testing-data/actions/workflows/main.yml)

A Snakemake workflow for creating long read (Nanopore with [`NanoSim`](https://github.com/bcgsc/NanoSim)) and short read (Illumina with [`seqkit sliding --circular-genome`](https://bioinf.shenwei.me/seqkit/) and [`mason_simulate`](https://www.seqan.de/apps/mason.html)) testing data for ecDNA analysis workflows.

## Usage

The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=dlaehnemann%2Fcreate-ecdna-testing-data).

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