This introductory workshop has been designed for the molecular biologist beginning analysis of Illumina data


This introductory workshop has been designed for the molecular biologist who wishes to perform basic analysis on small sets of Illumina data (i.e. a few lanes of sequences).

Many molecular biologists today do not have the bioinformatics skills to assess and analyse Illumina sequence data (aka Solexa sequencing data) for their projects. With the large uptake in this sequencing by the molecular biology community and a shortage in bioinformatics expertise, it has become beholden on the researcher to upskill. The largest barrier is the understanding of how to work with software in a command-line and/or linux environment. This course offers to the beginner a friendly hands-on approach to the basic analysis of Illumina data and working in the required environment.

The Course

This introductory course will take the participant slowly through a typical receipt of Illumina sequence data onto basic mapping to a reference genome, then introductory assembly into contigs. Knowledge of command line processing, linux OS and sequence software operation is not assumed and these key concepts will be taught during the course. By the end of the course participants should be able to map, assemble and view their mapped and assembled data.

Completion of this stage 1 course, or equivalent knowledge, will be a prerequisite to stage 2 courses (covering more detailed aspects of sequence analysis) currently being offered in this series of Workshops for Molecular Biologists.


The dates for this workshop are yet to be confirmed and will be determined by the level of interest. If you are interested in attending the Introductory Workshop in 2011 please contact Susan.

Registration includes attendance at the two day Introduction toIllumina Sequencing Workshop, morning teas, afternoon teas and lunches on both days. The registration fee includes course material as supplied.

Due to the hands-on nature of the Workshop and the limited number of computers available, the Workshop is capped at 20 participants. Registrations will be taken on a first-come, first served basis. Registration is confirmed when payment is received.

Registration button goes here.


To be decided.

Proposed Programme

The Workshop begins at 10am on the first day and finishes at 4pm on the second day.

Topics will include:

Basic Illumina Chemistry

  • Finding your way around Illumina data, files and formats
  • Viewing your data (basic command line in linux)
  • Introductory mapping
  • Viewing output
  • Sequence assembly

Basic Project Management


LesleyDr Lesley Collins has extensive experience in working with 'Solexa' (aka Illumina)-generated data and was instrumental in getting the Illumina Genome Analyser at Massey University up and running. Lesley is also familiar with sequence data generated by the 454 and SoLiD systems and the latest HiSeq technology from Illumina. Her hands-on approach has seen her tackle many of the Solexa-focused bioinformatics demands and she will share her experience and knowledge with you. Lesley was course-controller for the highly successful Massey Genome Service Workshops that ran in 2010.

Lesley is currently editing a book "RNA Infrastcructure and Networks" to be released in February.

Suggested Accommodation

HarringtonsFor those requiring overnight accommodation we suggest Harringtons Motor Lodge. Harringtons is New Zealand Qualmark 4 Star Plus - Enviro Silver accommodation and the closest accommodation to Massey University, less that 2km from campus.

The following rates have been secured for participants:

Executive Studio Suite - $120 per night for one person
One Bedroom Executive Spa Suite - $130 per night for one person
Extra person per room - $25 per person

To book and for more information on Harringtons please see their website. After booking please send a follow-up email to Bronwyn advising that you are attending the INGS meeting, referring to the reservation you have made, and the rate will be adjusted on your arrival at the accommodation.

Should you require transport from Harringtons to Massey University on the morning of the second day please indicate this on your registration form and we will arrange transport.


Course Controller: Dr Lesley Collins

For enquiries regarding workshop content please contact Lesley.
For questions regarding organisation please contact Susan.