ONLINE COURSE ' Genome Assembly and Annotation (GAAA01) We only have 4 places left on next week's course! https://www.prstats.org/course/genome-assembly-and-annotation-gaaa01/ 4th - 6th November 2024 Please feel free to share! COURSE OVERVIEW - Genome assembly is the process of piecing together fragments of DNA to reconstruct the original genome. The genome provides crucial information for understanding genetic structure, function and variation. In recent years, long-read sequencing technologies have revolutionized genome assembly. These long reads can span repetitive sequences and structural variations making genome assembly simpler but also reducing gaps and fragments in the genome, resolve repeats, help with the detection of structural variation as well as improved haplotype phasing. During this course we will look at data generated using PacBio and Oxford Nanopore, discuss the pros and cons of both sequencing technologies and the effect they might have on genome assembly. During the course we will look at different tools available to generate assemblies, focussing on de novo genome assembly. Polishing using short or long reads and the introduction of Hi-C sequencing can increase completeness of the genomes. At the difference steps during the assembly process we will look at the contiguity, completeness and correctness of the generated genomes, thereby evaluation the status of the genome. Once a genome has been assembled the next step is annotation. Genome annotation involves identifying and mapping locations of genes and other functional elements within the sequenced genome. We will take a look at the differences between prokaryote and eukaryote genomes and the tools available for annotation. We will talk about steps to improve annotation once the automatic annotation has been made. By the end of the course, participants should: Know the difference between Nanopore and PacBio data Be able to assembly genomes Be able to assess the generated genomes Assemble genomes integrating Hi-C data Know how to annotate a genome Please email oliverhooker@prstatistics.com with any questions. Oliver Hooker PhD. PR stats ----- ONLINE COURSE - Multivariate Analysis Of Ecological Communities Using R With The VEGAN package (VGNR07) https://www.prstats.org/course/multivariate-analysis-of-ecological-communities-using-r-with-the-vegan-package-vgnr07/ 31st - March - 4th April 2025 Please feel free to share! We encourage attendees to bring their own data, you will receive opportunities to discuss your data with the instructor throughout the course, if you would like guideline on how to organize your data prior to the course please ask oliverhoooker@prstatistica.com This course is suitable for researchers (PhD and MSc students, post-docs, primary investigators) and environmental professionals who are interested in implementing best practices and state-of-the-art methods for modelling species' distributions or ecological niches, with applications to biogeography, spatial ecology, biodiversity conservation and related disciplines. This 5-day course will cover R concepts, methods, and tools that can be used to analyze community ecology data. The course will review data processing techniques relevant to multivariate data sets. We will cover diversity indices, distance measures and distance-based multivariate methods, clustering, classification and ordination techniques using the R package VEGAN. We will use real-world empirical data sets to motivate analyses, such as describing patterns along gradients of environ-mental or anthropogenic disturbances, and quantifying the effects of continuous and discrete predictors. We will emphasise visualisation and reproducible workflows as well as good programming practices. The modules will consist of introductory lectures, guided computer coding, and participant exercises. The course is intended for intermediate users of R who are interested in community ecology, particularly in the areas of terrestrial and wetland ecology, microbial ecology, and natural resource management. You are strongly encouraged to use your own data sets (they should be clean and already structured, see the document: "recommendation if you participate with your data". Classes will run from 08:00 - 13:00 for the morning lecture and 14:00 - 16:00 for the practical (UK time) with an evening time session tbc for US, Canada etc. attendees. The course will be recorded and made available each day and will remain available for 28 days after the course for you to revisit any lectures. DAY 1 - Module 1: Introduction to community data analysis, basics of programming in R - Module 2: Diversity analysis, species-abundance distributions DAY 2 - Module 3: Distance and transformation measures - Module 4: Clustering and classification analysis DAY 3 - Module 5: Unconstrained ordinations: Principal Component Analysis - Module 6: Other unconstrained ordinations DAY 4 - Module 7: Constrained ordinations: RDA and other canonical analysis - Module 8: Statistical tests for multivariate data and variation partitioning DAY 5 - Module 9: Overview of Spatial analysis, and recent Hierarchical Modeling of Species Communities (HMSC) methods - Modules 10: Special topics and discussion, analyzing participants' data. Please email oliverhooker@prstatistics.com with any questions Oliver Hooker PhD. PR stats Oliver Hooker (to subscribe/unsubscribe the EvolDir send mail to golding@mcmaster.ca)