This hands-on workshop will introduce users of the R software environment to the techniques involved in generating reproducible, dynamic data analyses and reports. Using literate programming approaches, participants will learn to build automated reusable reports in R.
Southern Cross University – Plant Science Bioinformatics Support
Brief Project Description
The client is an Australian university research team with broad genomic experience and a special interest in genetics of Australian plants. QFAB is providing a full genomic assembly and analysis service on multiple organisms with direction and focus determined by the client.
Recent dramatic cost reductions in shotgun genomic sequencing now enable biologists to cheaply and quickly sample the DNA sequence of an interesting species, or selected individuals of special interest to their research interests. This “de novo” approach to whole-genome assembly from short shotgun reads is the most economical and fastest path to partial genome reconstruction for novel organisms but it is problematic when attempted without traditional guidance from physical clones or genetic maps. The “de novo” shotgun assembly method leads to fragmented and isolated plant nuclear chromosomal contigs which can be difficult to analyse. QFAB and the client assembled multiple genomes using different DNA assembly programs and then compared all assemblies against each other and to related species to identify the best product for subsequent genomic analyses.
QFAB fully reconstructed two organelle genomes and partially assembled multiple plant nuclear genomes. Organelle genomes have been shared privately and nuclear genomes for two Australian native species have been assembled and analysed for genes, repeats, microsatellite SSRs, and inter-species similarities. We have also prepared genome size estimates.