This section collects all the definitions and explanations of terms and concepts used in ggKbase.
Creating an analysis project Here are the steps for creating a new analysis project. Prior to these creation steps, you need to request the permission to create a project on ggKbase from the webmaster (webmaster@ggkbase.berkeley.edu). Go to https://ggkbase.berkeley.edu/projects/new Give it a name, slug and choose “analysis” in the dropdown menu Add organisms one by one…
Pyenv allows you to easily control your python environment. The TechTeam recommends that you set your biotite globally to Python 3, and set subdirectories to Python 2 when scripts require it. Thorough documentation and instructions on pyenv are here: https://github.com/pyenv/pyenv Quick start instructions for biotite: (Shortened from “Basic GitHub Checkout” on https://github.com/pyenv/pyenv) Checkout from GitHub…
Guide to NCBI WGS Submissions Intro: Join Banfield Lab NCBI. Slack Lily your email to be added to the group. Our lab’s contact is Larissa Brown. You may not email her directly until she contacts you, then you can reply to genomes@ncbi.nlm.nih.gov. Have NCBI annotate your genomes. Do not attempt to submit annotations unless absolutely…
ggKbase analysis of public genomes (or genomes from collaborators) for which we don’t have reads and assembly files requires an altered import preparation. The genomes will be concatenated into a mock metagenome, run through the normal metagenome preparation pipeline, and separated back into the original genomes using a scaff2bin file after import. 1. Put scaffold…