Introduction to Long-read Bioinformatics

30 Jan - 1 Feb 2023

Registration
 

OPEN: Register Here

Date

10am - 3pm each day (with 1hr for lunch)

Venue

Online

Places

20 for each workshop

You will be contacted by our finance team for full payment. Once payment is made, your place will be confirmed and full details sent by our training team.

Registration fee

£350 - University of Edinburgh Staff/students

£375 - Other University, or registered charity, staff/students

£400 - Industry staff

Information

Contact our training team

 

Overview

Whole genome sequencing (WGS) has been revolutionised by the development of long-read sequencing technologies in the last few years. Driven in no small part by Oxford Nanopore technologies (https://nanoporetech.com/and Pacific Biosciences, HiFi (https://www.pacb.com/technology/hifi-sequencing/), we now have the ability to sequence long (mb+) single-molecule DNA fragments. Although these developments are expected to alleviate numerous computational challenges surrounding genome analysis they also bring some interesting bioinformatics challenges to which we have to adapt in order to get the most from this powerful technology.

This exciting new course aims to introduce the principles and practice using long-read data analysis with focus on Oxford Nanopore data. We will present the cutting edge software and best practices tried and tested by our expert bioinformaticians here at Edinburgh Genomics.

Who this course is for

Aside from a basic understanding of molecular biology, attendees must have a working knowledge of how to use the Linux BASH command line - our 1-day "Linux for bioinformatics" course is a suitable background.

 


"Fantastic long reads bioinformatics workshop from @edgenome, superbly setup, good mix of theory and hands-on with @nanopore data.

Also @urmi208 is a brilliant instructor, effortlessly handling a very mixed skills bunch of people - and all that, online, hats off!" (May 2021)


 

Instructor

Urmi Trivedi - Bioinformatics Team Leader, Edinburgh Genomics

Heleen De Weerd - Bioinformatician/Analyst, Edinburgh Genomics

Workshop format

The workshop consists of presentations and hands-on tutorials.

 


Topics covered

  • Introduction to long read sequencing technologies
  • Long read data pre-processing (Nanopore + PacBio)
  • Mapping to a reference genome (minimap2)
  • Structural variant detection using long reads (NGMLR, sniffles, cuteSV, SURVIVOR, IGV)
  • De novo genome assembly using long reads (flye, Redbean)
  • Assessment of genome assembly (QUAST/BUSCO)
  • Polishing of genome assembly (MarginPolish/HELEN)