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. From these videos you will learn how to do the following:

  • Upload your contig files to the private PATRIC workspace and initiate a Genome Annotation Service job

  • Access and interpret the results from the annotation job

  • Download the annotated genome files

  • Examine the annotated genome using PATRIC tools

  • Get help if you have problems using the service

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. Relevant references are provided at the bottom of this page.

1. Uploading contig files to the PATRIC workspace (12:08)

2. Submitting a job to the PATRIC Genome Annotation Service (7:08)

3. Reviewing the resulting Genome Report (21:33)

4. Downloading generated files (11:06)

5. Viewing your annotated genome in PATRIC (16:53)

6. Finding help or reporting problems with the service (4:26)

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.