Perl is a computing language which has become popular for bioinformatics due to how it can be used to quickly filter through large amounts of data. This Workshop is a two day hands-on introduction to Perl Programming and
application to Next Generation Sequencing analysis


7 and 8 July 2011
10am on 7 July to 4pm on 8 July
Te Manawa, 326 Main St, Palmerston North


Perl is a computing language which has become popular for bioinformatics due to how it can be used to quickly filter through large amounts of data. Analysis of Next Generation Sequencing results, (especially Illumina and SOLiD data) can more easily managed if Perl programs are used to pick out and analyse targeted datasets. Although often seen as the realm of bioinformaticians, Perl is not a hard language to learn and is one of the most common computing languages used in genomics. This workshop has been designed for the absolute beginner in Perl programming with a focus on using Perl in the analysis of NGS data. Previous knowledge of computer programming or scripting languages is not required.

Participants will be required to bring their own laptop upon which Perl has been previously installed (detailed instructions on how to do this will be provided closer to the date). This will ensure that the Perl environment is correctly installed for the participant to do analysis on their own data after the workshop. Example data from NGS applications will be provided at the workshop, but Perl skills taught here will be applicable to other data.


Registration for this Workshop is capped at 15 participants. Registrations will be taken on a first-come, first served basis. Registration is confirmed when payment is received.

The cost to attend the one day workshop is NZ$645 +15% GST per registrant ($741.75 incl GST).

The registration form lists optional transport from the airport to Te Manawa (departing from the airport at 9.45am on the first day) and from Te Manawa to the airport (leaving the workshop venue at 4.10pm on the second day). Should you wish transport to be arranged for you please indicate this on the registration form. The cost of the shuttle service is $9 each way.

Registration includes attendance at the two day Perl Workshop, morning teas, lunches, afternoon teas and dinner at a chosen local restaurant on the evening of 7 July. The registration fee includes course material as supplied.

If you try to register for the Perl Workshop and the Workshop is full please email Susan and let her know of your interest to attend a future Perl Workshop. You will be contacted when the next Perl Workshop is scheduled.

Course Plan

The Workshop will start on the first day at 10.10am, with morning tea served from 9.45am, and finish at 4pm on day two. The programme is yet to be finalised but the following is an indication of what will be covered:

Topics will include:

  • Introduction to Perl and NGS
  • Perl Basics
  • Filtering Sequence Data with Perl
  • Filtering Mapping Data with Perl
  • Quick introduction to BioPerl and other Perl modules


The Workshop will be held at Te Manawa which is the local Palmerston North Museum in the middle of Palmerston North at 326 Main St. Map.


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

QuestQuest Palmerston North is a purpose-built 4.5 Qualmark Star property located on in the TSB Building on the Square in the CBD of Palmerston North. It offers a range of studio, one and two bedroom interconnecting apartments. There is an internet connection in every room with the connection costing $5 per hour or $15 per day. While staying at Quest you get complimentary use of the gym at Palmerston North Squash Club which is just 2 min walking distance from our property. The Quest is within easy walking distance of Te Manawa. Map.

The following rates have been secured for participants:

Studio Apartment (king bed) - $145 incl GST per night
Studio Apartment (two single beds) - $155 incl GST per night
One Bedroom Apartment (king or queen bed) - $175 incl GST per night
One Bedroom Apartment with rollaway bed- $185 incl GST per night

To secure these preferential rates please phone Quest on 06 357 2697 and identify yourself as a Perl Workshop attendee when making your booking. For more information on Quest Palmerston North please see their website.


For any questions regarding the Progamme for the Workshop please contact Lesley.
For any questions on the organisation of the Workshop please contact Susan.