Course Content

Welcome to the Bioinformatics of Single Cell Genomes Course!

We're excited to have you. Here's some information to get us going.

Lesson Resources

The majority of course lessons are available through our course GitHub organization, the ‘Bigelow-SCG-Course’ on github. There, you'll find a number of different repositories for lessons we'll be covering this week. As we begin a lesson, we'll pull down the appropriate course material from this webpage.

Repositories are also linked to on the lesson links page of this website.

Computational Environment

For ease of use, we have put together an online virtual HPC environment that we will all be using this week. It is a ‘jupyterhub’.

To get set up in the course jupyterhub, see the hub setup page.

Lesson structure

Lessons for this course will generally follow a similar pattern. First, there will be a lecture and demo of how a tool is run. This will be followed by analysis of output data using a jupyter notebook. The purpose of these notebooks is to give participants analysis templates they may copy and play around with to learn about the types of outputs and analyses different bioinformatics software provide.

We encourage participants to explore on their own, and to take advantage of the computational environment we are providing to experiment with the tools we are presenting.

Course data

The main focus of this course is going to be on one particular plate of single amplified microbial genomes: AG-910. AG-910 is one of over 20 plates sequenced as part of the GORG-Tropics cell collection. It comes from sample BATS248 from the Bermuda Atlantic Time Series. Course data is available here