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Update README.md #180

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Expand Up @@ -11,21 +11,23 @@ For the complete TOSTADAS documentation, please see the [Wiki](https://github.co
**T O S T A D A S**
**T**oolkit for **O**pen **S**equence **T**riage, **A**nnotation, and **DA**tabase **S**ubmission

A portable, open-source pipeline designed to streamline submission of pathogen genomic data to public repositories. Reducing barriers to timely data submission increases the value of public repositories for both public health decision making and scientific research. TOSTADAS facilitates routine sequence submission by standardizing:
A portable, open-source pipeline designed to streamline submission of pathogen genomic data to public repositories. Reducing barriers to timely data submission increases the value of public repositories for both public health decision making and scientific research. TOSTADAS facilitates routine sequence submission by standardizing and automating:

+ Metadata Validation
+ Genome Annotation
+ File submission

The current release is tested with sequence data from Poxviruses and select bacteria but TOSTADAS is designed to be flexible, modular, and pathogen agnostic, allowing users to customize their submission of raw read data, assembled genomes, or both.
TOSTADAS is designed to be flexible, modular, and pathogen agnostic, allowing users to customize their submission of raw read data, assembled genomes, or both. The current release has been tested with sequence data from Poxviruses and select bacteria. Testing for additional pathogen is planned for future releases.

## Quick Start
❗ Note: If you are a CDC user, please follow the set-up instructions found here: [CDC User Guide](https://github.com/CDCgov/tostadas/wiki/CDC-User-Guide)

For non-CDC users, please follow the instructions below.
### 1. Clone the repository to your local machine
```
git clone https://github.com/CDCgov/tostadas.git
```
! Note: If you already have Nextflow installed in your local environment, skip ahead to step 5.
### 2. Install mamba and add it to your PATH

**2a. Install mamba**
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