Practical hands-on training in helminth genome analysis.

Helminths infections contribute significantly to the burden of neglected tropical diseases (NTDs) in many low- and middle- income countries (LMICs). Despite important efforts to tackle these diseases through mass drug administration programs and other methods of control and containment, NTDs due to helminths such as schistosomiasis and soil-transmitted helminthiases continue to be among the most debilitating and morbidity-causing diseases in LMICs adding significantly to the economic burden in the strained economies. Moreover, decreased susceptibility to the most used chemotherapies is emerging in the field, raising concerns about the rise of drug-resistant helminths.

Advances in sequencing technologies have enabled the production of draft and high-quality genome assemblies for the most important disease-causing helminths. In addition, reduced costs of next-generation sequencing (NGS) techniques make sequencing accessible to the wider scientific community of researchers and organisations, providing unprecedented access to genomics. Data manipulation and computational analyses are still the main challenges that limit the realization of maximum benefit and appropriate interpretation of these data.

The Helminth Bioinformatics course aims to equip participants with the skills needed to access, analyse and display large-scale genomic data. The course will provide hands-on training in read mapping, transcriptomics and genetic variation analysis, all tailored to address the challenges presented by large helminth genomes. Participants will acquire basic and advanced techniques in bioinformatics while getting familiar with computer command-line languages and public data repositories.

The programme is aimed at researchers at various levels including Senior Research Assistants, PhD Students, Postdoctoral Researchers, Laboratory Scientists and Clinical Scientists.

This week-long course is free to attend and open to applicants based in Asia involved in helminth-related research. The course will be taught in English.

The practical computational sessions will be taught exclusively through Unix/Linux. Participants should have some familiarity with the Linux operating system. This will allow participants to fully benefit from the course. There are numerous online introductory tutorials to the UNIX/Linux operating system and command line, including:

https://www.futurelearn.com/courses/linux-for-bioinformatics http://www.ee.surrey.ac.uk/Teaching/Unix http://swcarpentry.github.io/shell-novice/

Course website

You may find a short online course on Introduction to Genomics beneficial for a quick recap and preparation. The course was designed specifically for the participants of Helminth Bioinformatics course, but is open for all. The course is on KKUMedX online-learning platform. The instruction on how to register is available here.

• Anna Protasio, University of Cambridge, UK
• Arporn (Koi) Wangwiwatsin, Khon Kaen University, Thailand
• Faye Rodgers, Wellcome Sanger Institute, UK
• Heerman Kumar, Monash University, Malaysia
• Isheng Jason Tsai, Academia Sinica, Taiwan
• Kevin Howe, EBI, UK
• Martin Aslett, WGC Advanced Courses, UK
• Matt Berriman, Wellcome Sanger Institute, UK
• Sarah Geiger, National University of Singapore (NUS) & Genome Institute of Singapore (GIS)
• Steve Doyle, Wellcome Sanger Institute, UK
• Jutarop Phetcharaburanin, Khon Kaen University, Thailand
• Sirinya Sitthirak, Khon Kaen University, Thailand

• Monday
  • WormBase Parasite 1
  • Unix Scripting
• Tuesday
  • WormBase Parasite 2
  • Project Introduction and Planning
• Wednesday
  • R and RStudio
  • Genome Variation
• Thursday
  • Transcriptomics
• Friday
  • Project & presentations

Download here

Module 1 - WormBase Parasite 1
- Introductory presentation
- Online manual
- Manual PDF version

Module 2 - Unix Scripting
- Introductory presentation
- Online manual
- Manual PDF version

Module 3 - WormBase Parasite 2
- Introductory presentation
- Online manual
- Manual PDF version

Module 4 - Project Introduction and Planning
- Introductory presentation
- Online manual
- Manual PDF version

Module 5 - R and RStudio
- Introductory presentation
- Online manual
- Manual PDF version

Module 6 - Genome Variation
- Introductory presentation
- Online manual
- Manual PDF version

Module 7 - Transcriptomics
- Online manual
- Manual PDF version

Module 8 - Project
- Online manual
- Manual PDF version

Appendix

• Creating a shared folder between your computer and VM
• Finding and download sequence data from public repository
• Downloading GO term annotation from WormBase ParaSite and formatting it for topGO

Any reuse of the course materials, data or code is encouraged with due acknowledgement.

This work is licensed under a Creative Commons Attribution 4.0 International License.