• Event
  • Scientific training

Genome Annotation Workshop 2021

This 3-day course will help to provide scientists with an overview of eukaryotic genome annotation approaches, covering advances in Next Generation Sequencing (NGS) technologies, transcriptome assembly, best practice guidance for building gene models utilising short and long read sequencing data or cross species proteins, how to integrate and assess different gene models and create a publication/release ready gene set.

Start date:

13 April 2021

End date:

15 April 2021

Time:

10h00 - 15h00

Venue:

Online (via Zoom)

Registration deadline:

14 March 2021

Cost:

£150

About the event.

About this workshop

The value of a genome assembly depends heavily on the quality of its accompanying genome annotation. Automated procedures for annotation are therefore required that are robust to different genome characteristics and can efficiently and accurately annotate not only high-quality reference genomes but also large, fragmented “draft” genomes. The benefits of high-quality annotated genomes is well known - more accurate and complete annotation enables better interpretation of genome information within and across species, aiding researchers in their work to understand biological processes.

Earlham Institute (EI) has developed a number of tools to support high quality annotation (including Mikado and Portcullis). Mikado (PMID: 30052957) is an open-source Python3 and Cython program that provides a framework for integrating transcripts from multiple sources into a consolidated set of gene annotations, while Portcullis (PMID: 30418570) is a tool to aid accurate splice junction detection. Both tools were utilised to aid the annotation of the wheat genome as part of the International wheat genome sequencing consortium (IWGSC, PMID: 30115783) and are being used to support EIs work in large collaborative genome sequencing projects such as the Wheat 10+ and Darwin Tree of Life

In this 3-day virtual course, you will:

  • Get an overview of Next Generation Sequencing technologies relevant to genome annotation
  • Gain a deeper understanding of the benefits of each platform and have the confidence to select the right platform or combination of platforms for your project
  • Understand what to look for in a sample that will pass quality control and that will likely succeed in producing viable sequencing data, in particular expectations for pre-made libraries
  • Learn how to assess the quality of RNA-Seq data
  • Learn about de novo and reference guided transcriptome assembly and steps for processing long read data
  • Learn about alternative approaches for annotating protein coding genes in eukaryotic species
  • Hands on experience of annotation tools including tools and pipelines developed at the Earlham Institute.

Who is this event for?

Advanced PhD students and post-doctoral researchers who are undertaking projects involving annotating a genome assembly or generating transcriptome assemblies.

Prerequisites

You are expected to have experience with using the command line and will be looking to improve your awareness of different approaches and pipelines.

Programme.

Day 1 - 13 April 2021

Time

Topic

10:00 - 10:45

Welcome, course overview and flash presentations from participants

10:45 - 11:15

Introduction to NGS technologies for Genome Annotation -Dr Karim Gharbi

11:15 - 11:30

Break

11:30 - 12:00

Practical considerations for isolating high-quality RNA - Leah Catchpole

12:00 - 12:30

Data QC and overview of data formats

12:30 - 13:30

Lunch Break

13:30 - 14:00

A practical guide to De Novo transciptome assembly

14:00 - 15:00

Reference-guided transcriptome assembly

Day 2 - 14 April 2021

Time

Topic

10:00 - 11:15

Hands-on: Transcriptome assembly

11:15 - 11:30

Break

11:30 - 12:30

Hands-on: Transcriptome assembly

12:30 - 13:30

Lunch Break

13:30 - 14:15

Long Read Data Processing

14:15 - 15:00

Case Study: Long Read Data - Wilfried Haerty

Day 3 - 15 April 2021

Time

Topic

10:00 - 10:45

Genome Annotation - Building high quality gene models

10:45 - 11:15

Hands-on: Genome Annotation

11:15 - 11:30

Break

11:30 - 12:30

Hands-on: Genome Annotation

12:30 - 13:30

Lunch Break

13:30 - 14:15

Assesing the quality of a genome annotation

14:15 - 14:45

Building gene Families and assessing gene structure - Anil Thanki

14:45 - 15:00

Event Close and Feedback

Further information.

Please carefully review our standard online event booking terms and conditions prior to registering for this event. Completing an online registration and associated payment process will mean that you are bound by these terms and conditions. Any supplemental terms or changes to these conditions on a per event basis will be included on this page. If you have any queries regarding our events or in relation to your booking, please contact us at training@earlham.ac.uk

  • Register today.

Registration deadline: 14 Mar 2021 - 23:45

Participation: First come, first served