LM3601 Molecular Biotechnology and Genomics (MBG) course

Online

Nov 12 - Dec 17, 2020

1:45 pm - 5:30 pm

Instructors: Raúl A. Ortiz-Merino, Marcel van den Broek, Jean-Marc Daran

Helpers: Raúl A. Ortiz-Merino, Marcel van den Broek

General Information

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Good Enough Practices for Scientific Computing".

Who: The course is aimed at masters students from TU Delft. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Check brightspace for Zoom link. Get directions with OpenStreetMap or Google Maps.

When: Nov 12 - Dec 17, 2020. Add to your Google Calendar.

Requirements: Participants must have acces to a computer with Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). In case of having a windos system, make sure to have access to PuTTY or otherwise install it by going to the installation page. Other specific software packages required can be consulted (listed below).

Code of Conduct: Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Contact: Please email J.G.Daran@tudelft.nl for more information.

Schedule

Day 1: November 12

13:45 - 14:30 -------- General Introduction -------
Project Organization and Management
14:30 - 14:45 Break
14:45 - 15:30 Connecting to the cloud
15:30 - 15:45 Break
15:45 - 16:30 Introduction to the Command Line 1
16:30 - 16:45 Break
16:45 - 17:30 Introduction to the Command Line 2

Day 2: November 19

13:45 - 14:30 -- Data Wrangling and Processing 1 --
Introduction
14:30 - 14:45 Break
14:45 - 15:30 FastQC
15:30 - 15:45 Break
15:45 - 16:30 Trimmomatic
16:30 - 16:45 Break
16:45 - 17:30 Both

Day 3: November 26

13:45 - 14:30 -- Data Wrangling and Processing 2 --
Alignment
14:30 - 14:45 Break
14:45 - 15:30 Processing
15:30 - 15:45 Break
15:45 - 16:30 Variant Calling
16:30 - 16:45 Break
16:45 - 17:30 Visualisation

Day 4: December 3

13:45 - 14:30 --------- Genome Assembly 1 ---------
Quality control
14:30 - 14:45 Break
14:45 - 15:30 Spades PE
15:30 - 15:45 Break
15:45 - 16:30 Spades MP
16:30 - 16:45 Break
16:45 - 17:30 Annotation

Day 5: December 10

13:45 - 14:30 --------- Genome Assembly 2 ---------
ONT Assembly, polishing and annotation
14:30 - 14:45 Break
14:45 - 15:30 Alignment, visualisation
15:30 - 15:45 Break
15:45 - 16:30 Comparisons
16:30 - 16:45 Break
16:45 - 17:30 Annotation

Day 6: December 17

13:45 - 17:30 ------------- Evaluation ------------

Syllabus

Project Organization and Management

Introduction to the Command Line

Data Wrangling and Processing for Genomics 1

Data Wrangling and Processing for Genomics 2

Genome Assembly 1

Genome Assembly 2

Setup

To participate in a Data Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The setup instructions for the Data Carpentry Genomics workshops can be found at the workshop overview site

.