Welcome to Flapjack. We have created a series of Flapajck training tutorials that explain Flapjack operation and analysis features. We aim to deliver Flapjack hands on training with real data examples resulting in users gaining valuable process and analysis understanding. This training will combine videos and examples along with links to the relvant Flapjack help pages which will help give you a working knowledge of how to use Flapjack. We hope that this training will act as a springboard to help you start to explore your data and explore all the tools and features that Flapjack can offer.
There are tutorials covering Flapjack basic operation, input files, importing & data navigation and data views and visualisation. Additional analysis tutorials which we are developing will cover similarity matrix & Dendrogram creation, Marker assisted backcrossing, F1 analysis, Forward breeding & Pedigree verification and will be available soon.
Each tutorial has its own video that explains and demonstrates concepts we want to convey, some will have additional information then a series of tasks and answers that will let you get experience in using Flapjack using real data.
This training has been designed for you to carry out at your own pace. Each section is self-contained and while we recommend that you carry each out in series, you can do this training at your own pace and come back to sections if you are unsure or just want to try the user exercises again at the end of each section.
For all information on Flapjack look at https://ics.hutton.ac.uk/flapjack which will give you an overview of the application as well as download links, help and documentation, most recent update features and publication information.
If you have any questions about Flapjack or just want to chat through the benefits and features that it can offer, please just drop us an email to flapjack@hutton.ac.uk. Software updates will be posted here https://twitter.com/cropgeeks and you can also log bugs and feature requests on our Github page https://github.com/cropgeeks/flapjack
The original Flapjack publication will give you a bit of background to the project and is worth a read but please remember that Flapjack has developed significantly since 2010 and now has many more useful features!
Milne I, Shaw P, Stephen G, Bayer M, Cardle L, Thomas WTB, Flavell AJ and Marshall D. 2010. Flapjack – graphical genotype visualization. Bioinformatics 26(24), 3133-3134.
In late 'noughties' there was a huge increase in genetic information available to researchers that was driven by next generation sequencing technologies (NGS) which drove down the cost of large sequencing projects. High throughput genotyping platforms were developed to help reduce genomic and data complexity and software to handle such data volumes was required.
Flapjack was developed to handle high throughput single nucleotide polymorphism or SNP data and Genotyping by Sequencing or GBS data from various platforms. QTL and Phenotype data can also be added to flapjack to provide analysis options and interactions.
Based on the input of map, genotype and trait data Flapjack can provide several alternative graphical genotype views with individual alleles coloured by state, frequency or similarity to a given standard line. Flapjack supports a range of interactions with the data, including graphically moving lines or markers around the display, insertions, or deletions of data, and sorting or clustering of lines by either genotype similarity to other lines, or by trait scores. Any map-based information such as QTL positions can be aligned against graphical genotypes to identify associated haplotypes. Flapjack also allows for analysis methods to run over the data, such as calculating similarity matrices, running PCoA calculations, or the generation of statistics to help with marker assisted back crossing or pedigree verification of F1s.
Flapjack has been developed by the Information and Computational Sciences Department at the James Hutton Institute just outside of Dundee in Scotland. It and was published in Bioinformatics in 2010. And now has over 5500 users worldwide.
Flapjack is updated regularly to provide added functionality and software improvements. We are also keen to get feedback and hear from users on how we can improve the platform. Originally Flapjack was created to meet the needs of barley and potato work being carried out in Scotland but has now expanded to cover many different crops from around the world.
Flapjack accepts tab delimited files containing the following data: Genotype, Map, QTL and Phenotype. Full details are provided in an associated tutorial.
All results are saved in a Flapjack project format file and can also be exported as raw data or graphically as image files. We have devised efficient data storage structures that provide high-speed access to any subset of the data, resulting in fast visualization regardless of the size of the data.
Flapjack is available to download from the James Hutton Institute, Information and Computer Sciences web pages. https://ics.hutton.ac.uk/flapjack/download-flapjack/ 3 installers are available, Windows (64 bit), MacOS and if you prefer using the command line a Linux (64 bit) version exists. Full details are provided in an associated tutorial.
Contact us, please get in touch and we can give an extended demo or talk you through using Flapjack with your data or how you can help be part of the Germinate community. Contact details are at the top of each of these training sections.
Next Steps: We have learned a bit of background, now let's have a look at downloading and familiarising ourselves with Flapjack in Session 2
This training has been created under the Templeton World Charity Foundation, Inc. Grant ID TWCF0400 'Safeguarding crop diversity for food security: Pre-breeding complemented with Innovative Finance' which is managed by the Crop Trust. This training is free to use and released under a non-restrictive open source licence.