Genome Annotation Workshop 2021

Registration is now closed for this event as we have reached capacity. If you wish to be placed on the waiting list, please email training@earlham.ac.uk

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. 

This training forms part of our BBSRC National Capability in Advanced Training