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Data Wrangling with EnsemblLite and Cogent3

We will show how EnsemblLite, cogent3 and associated tools can greatly simplify getting sequence data for analyses.

Time, Location

The workshop is in Puerto Vallarta!

Please fill in the survey to help us understand your background and motivation.

The time: 11am-4pm, July 7th 2024

The location: TO FILL IN

Workshop Content

We will be using Docker to provide the computing environment, so the topics we will cover are (click to expand each section).

Getting data with EnsemblLite

• Configure EnsemblLite to download and install genome(s)
• Sampling gene sequences and their meta-data
• Sampling homology data
• Sampling from whole genome alignments

Processing data using Cogent3

- Using cogent3 to process the exported data

Contributing to open source software

- Explanation of standard practice for contributing to open source software for science - Vote on new EnsemblLite feature(s) to be added then let's do a code sprint to add them!

Prerequisites

All you need for this workshop is a laptop, familiarity with command-line applications and Python.

Ideally, you should be able to install software on your machine (see Computer Setup page).

More workshop information

Please keep checking back here for updates regarding physical location and setting up your computer before the workshop.

We look forward to seeing you there!

👾 The EnsemblLite & cogent3 development teams.