# nf-core/viralrecon: Documentation

The nf-core/viralrecon documentation is split into the following files:

1. [Installation](https://nf-co.re/usage/installation)
2. Pipeline configuration
    * [Local installation](https://nf-co.re/usage/local_installation)
    * [Adding your own system config](https://nf-co.re/usage/adding_own_config)
    * [Reference genomes](usage.md#reference-genomes)
3. [Running the pipeline](usage.md)
4. [Output and how to interpret the results](output.md)
5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
