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README.md

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<!-- [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23viralgenie-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/viralgenie)-->
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> [!TIP]
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> Make sure to checkout the [viralgenie website](https://joon-klaps.github.io/viralgenie/) for more elaborate documentation!
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## Introduction
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**Joon-Klaps/viralgenie** is a bioinformatics best-practice analysis pipeline for reconstructing consensus genomes and to identify intra-host variants from metagenomic sequencing data or enriched based sequencing data like hybrid capture.

docs/CONTRIBUTING.md

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- Tools installed
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- nf-core
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- Nextflow
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Devcontainer specs:
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- [DevContainer config](.devcontainer/devcontainer.json)

docs/README.md

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==}
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[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
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[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/Joon-Klaps/viralgenie)
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[![GitHub Actions CI Status](https://github.com/Joon-Klaps/viralgenie/actions/workflows/ci.yml/badge.svg)](https://github.com/Joon-Klaps/viralgenie/actions?query=workflow%3A%22nf-core+CI%22)
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[![GitHub Actions Linting Status](https://github.com/Joon-Klaps/viralgenie/actions/workflows/linting.yml/badge.svg)](https://github.com/Joon-Klaps/viralgenie/actions?query=workflow%3A%22nf-core+linting%22)
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<!-- [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23viralgenie-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/viralgenie)-->
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## Introduction
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![viralgenie-workflow](images/metromap_style_pipeline_workflow_viralgenie.png)
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