## Protocols and guides used in the computational biology module of BIO346 *Laboratory in Bacterial Pathogenomics* - [Navigating and Using GalaxyTrakr (and Galaxy)][1] - [*Salmonella* Serotyping][2] - [FastQC & Trimmomatic: Assessing & Filtering Illumina Short Read NGS Data in GalaxyTrakr][3] - [File Naming Conventions][4] - [*de novo* Assembly of Genomes using SPAdes on GalaxyTrakr/Moving Data Library Files to a New GalaxyTrakr History][5] - [Assessing Assembly Quality Using QUAST and Bandage][6] - [Ordering and viewing assembled contigs][7] - [Gene Annotation][8] - [RAST Gene Annotation Draft Protocol][9] - [Antimicrobial Resistance Gene Detection][10] - [Miscellaneous Gene Detection][11] - [Getting Started with Enterobase][12] - [Bioinformatics Lab Notebook template][13] [1]: https://docs.google.com/document/d/1KOpggBR3MpYYArNATVybgs89QZZaIe5j0gvmP3GT_SM/edit?usp=sharing [2]: https://docs.google.com/document/d/1BmZTSdf22g-PN1wNvpgy-1sPRyzQGfcqONwnP-CJ2Wk/edit?usp=sharing [3]: https://docs.google.com/document/d/1GLB0joLw6te6BvtpBMd08OoosI8Wp8YqKHrzVJTEiHM/edit?usp=sharing [4]: https://docs.google.com/document/d/16FmQvgttgOTzhbDLXcyg_3gh0oIYEcnhvEp0uMR4_48/edit?usp=sharing [5]: https://docs.google.com/document/d/1AEXl9IWZmHXQsYrKl1RiEnTwrFD5IfqccJ14jcE1bic/edit?usp=sharing [6]: https://docs.google.com/document/d/1t9IBF2Mg9W2lU-sG6_ELzS8kJKrXLXZkDbLoJMmTeXM/edit?usp=sharing [7]: https://docs.google.com/document/d/1bJSrRmS7kwnHbI6XRWSDXVoEeOC9YZjAk2U4vDkGC6Q/edit?usp=sharing [8]: https://docs.google.com/document/d/1NkU2G37Lg6NVGsf4rllZzShWpippWF5ZvTDdqj2r1TI/edit?usp=sharing [9]: https://docs.google.com/document/d/1O8cWtS6gXOn3v5Cb2WcqqPD3-PMrddfrUe1yugbq0sY/edit?usp=sharing [10]: https://docs.google.com/document/d/1VvHlpwOHGnIWmPdHmMt9Raba2aFmR_eLMCFmGtDlnSk/edit?usp=sharing [11]: https://docs.google.com/document/d/1nZbBQFSNmGQXE2svvh7DZpSf9wYdVXB0GeLdKwJYbPA/edit?usp=sharing [12]: https://docs.google.com/document/d/1NbILHMeHwj1bQr0QOjjlquD-_7T6REbnjwkJ-4f-P9U/edit?usp=sharing [13]: https://docs.google.com/document/d/1T7ZKtNEapD-IIG_glnoZaz00rDus4FpyV5mdGh-j0zE/edit?usp=sharing