# Tutorial: Genome Annotation Service

## Overview
This set of short videos provides a step-by-step demonstration of using the PATRIC Genome Annotation Service to annotate a genome from a set a bacterial contig files.

1. [Uploading contig files to the PATRIC workspace (12:08)](#annotation1)
2. [Submitting a job to the PATRIC Genome Annotation Service (7:08)](#annotation2)
3. [Reviewing the resulting Genome Report (21:33)](#annotation3)
4. [Downloading the generated files (11:06)](#annotation4)
5. [Viewing your annotated genome in PATRIC (16:53)](#annotation5)
6. [Finding help or reporting problems with the service (4:26)](#annotation6)


### See also
* [Genome Annotation Service](https://patricbrc.org/app/Annotation)
* [Genome Annotation Service Tutorial](https://docs.patricbrc.org/tutorial/genome_annotation/annotation.html) (document)

## Using the Genome Annotation Service

Links to the videos are provided below.  They can also be viewed in order in the [PATRIC YouTube channel playlist](https://www.youtube.com/watch?v=IOo3POYtCKs&list=PLsstVALeacELn_vRu1tm7654_pdnm6lQT). Relevant references are provided at the bottom of this page.

<a name="annotation1"></a>
##### 1. Uploading contig files to the PATRIC workspace (12:08)
<iframe width="560" height="315" src="https://www.youtube.com/embed/IOo3POYtCKs" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 
<a name="annotation2"></a>
##### 2. Submitting a job to the PATRIC Genome Annotation Service (7:08)
<iframe width="560" height="315" src="https://www.youtube.com/embed/dnopNXkJM6U" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="annotation3"></a>
##### 3. Reviewing the resulting Genome Report (21:33)
<iframe width="560" height="315" src="https://www.youtube.com/embed/R4nWHC2921A" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="annotation4"></a>
##### 4. Downloading generated files (11:06)
<iframe width="560" height="315" src="https://www.youtube.com/embed/2oiBZIuQAXE" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="annotation5"></a>
##### 5. Viewing your annotated genome in PATRIC (16:53)
<iframe width="560" height="315" src="https://www.youtube.com/embed/YIO-ssRz42g" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="annotation6"></a>
##### 6. Finding help or reporting problems with the service (4:26)
<iframe width="560" height="315" src="https://www.youtube.com/embed/Byq98NNxWQ4" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

## References
* Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason JA 3rd, Stevens R, Vonstein V, Wattam AR, Xia F. (2015). RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Scientific reports 5: 8365.
* Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C, Conrad N, Dietrich EM, Disz T, Gabbard JL, Gerdes S, Henry CS, Kenyon RW, Machi D, Mao C, Nordberg EK, Olsen GJ, Murphy-Olson DE, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Vonstein V, Warren A, Xia F, Yoo H, Stevens RL. (2017) Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res. 45(D1): D535-D542.