Comparative genomics (CMGN01) https://www.prinformatics.com/course/comparative-genomics-cmgn01/
This course will be delivered by Dr. Fritz Sedlazeck and Dr. Matthias Weissensteiner from the 29th April - 3rd May 2019 in Glasgow city centre COURSE OVERVIEW This course will introduce biologists and bioinformaticians to the field of comparative genomics. The course will give a deeper understanding on the advantages and disadvantages of each of approach in general to enabling an informed decision of study design for the participants for future studies and learn the cutting edge approaches to process state of the art data sets. Different techniques will be introduced to identify single nucleotide polymorphism (SNP) and structural variations (SVs) as well as the annotation of these variations and the assessment for their functional impact. We will give a broad introduction on how to: 1) Process short and long read data based on multiple NGS data sets including mapping and de novo assembly 2) Detect SNP and Structural Variations using de novo assembly, short or long read mapping 3) Assess the impact of the detected variations 4) Perform population genetic analysis between multiple samples to obtain a deeper insight into these variants. Furthermore, we will teach on how to install and manage these methods and give an introduction in Cloud computing. This will enable the participants to set up efficient pipelines on their own institutions. The course will conclude with the participants being aware of the state of the art approaches and a deepened knowledge to decide which study design is the optimal for future studies . COURSE PROGRAMME Day 1: Intro + Assembly Lecture: Setting up and getting familiar with the system Data types, technology overview De novo assembly Practical: Getting used to the environment Manipulating read data (filtering, trimming, etc.) Short vs. long read assembly Subprocessing: QC, polishing of de novo assemblies Day 2: Assembly quality + polishing ; RNA-Seq + short read mapping Lecture: How it works behind the scenes Data formats Common methods Practical: Insight in short read mappers Long read mapping SNP calling RNA-Seq expression Day 3: SNP? + SVs detection (Assembly, Read based, phasing?) Lecture: Structural variation detection Methods to detect SV Current state of the art of technologies. Practical: Short read based SV calling Long read based SV calling Assembly based SV calling Comparing and filtering SVs Annotation of SVs Day 4: Larger analysis over multiple data set and assessment of mutations over FST Lecture: Evolutionary genetics of structural variation Study design and sampling schemes Limitations Practical: Downstream analysis: Descriptive (SNP & SV density) PopGen (Fst, genetic diversity) Outlier analysis Day 5: Summary and conclusion Group discussions, final questions and overall summary (own data questions if time permits) Email [email protected] Check out our sister sites, www.PRstatistics.com (Ecology and Life Sciences) www.PRinformatics.com (Bioinformatics and data science) www.PSstatistics.com (Behaviour and cognition) UPCOMING COURSES 1. November 5th – 8th 2018 PHYLOGENETIC COMPARATIVE METHODS FOR STUDYING DIVERSIFICATION AND PHENOTYPIC EVOLUTION (PCME01) Glasgow, Scotland, Dr. Antigoni Kaliontzopoulou https://www.prstatistics.com/course/phylogenetic-comparative-methods-for-studying-diversification-and-phenotypic-evolution-pcme01/ 2. November 19th – 23rd 2018 STRUCTUAL EQUATION MODELLING FOR ECOLOGISTS AND EVOLUTIONARY BIOLOGISTS (SEMR02) Glasgow, Scotland, Dr. Jonathan Lefcheck https://www.prstatistics.com/course/structural-equation-modelling-for-ecologists-and-evolutionary-biologists-semr02/ 3. November 26th – 30th 2018 FUNCTIONAL ECOLOGY FROM ORGANISM TO ECOSYSTEM: THEORY AND COMPUTATION (FEER01) Glasgow, Scotland, Dr. Francesco de Bello, Dr. Lars Götzenberger, Dr. Carlos Carmona http://www.prstatistics.com/course/functional-ecology-from-organism-to-ecosystem-theory-and-computation-feer01/ 4. December 3rd – 7th 2018 INTRODUCTION TO BAYESIAN DATA ANALYSIS FOR SOCIAL AND BEHAVIOURAL SCIENCES USING R AND STAN (BDRS01) Glasgow, Dr. Mark Andrews https://www.psstatistics.com/course/introduction-to-bayesian-data-analysis-for-social-and-behavioural-sciences-using-r-and-stan-bdrs01/ 5. January 21st – 25th 2019 STATISTICAL MODELLING OF TIME-TO-EVENT DATA USING SURVIVAL ANALYSIS: AN INTRODUCTION FOR ANIMAL BEHAVIOURISTS, ECOLOGISTS AND EVOLUTIONARY BIOLOGISTS (TTED01) Glasgow, Scotland, Dr. Will Hoppitt https://www.psstatistics.com/course/statistical-modelling-of-time-to-event-data-using-survival-analysis-tted01/ 6. January 21st – 25th 2019 ADVANCING IN STATISTICAL MODELLING USING R (ADVR08) Glasgow, Scotland, Dr. Luc Bussiere, Dr. Tom Houslay http://www.prstatistics.com/course/advancing-statistical-modelling-using-r-advr08/ 7. January 28th– February 1st 2019 AQUATIC ACOUSTIC TELEMETRY DATA ANALYSIS AND SURVEY DESIGN Glasgow, Scotland, VEMCO staff and affiliates https://www.prstatistics.com/course/aquatic-acoustic-telemetry-data-analysis-atda01/ 8. February 4th – 8th 2019 DESIGNING RELIABLE AND EFFICIENT EXPERIMENTS FOR SOCIAL SCIENCES (DRES01) Glasgow, Scotland, Dr. Daniel Lakens https://www.psstatistics.com/course/designing-reliable-and-effecient-experiments-for-social-sciences-dres01/ 9. February 11th – 15th 2019 REPRODUCIBLE DATA SCIENCE FOR POPULATION GENETICS Glasgow, Scotland, Dr. Thibaut Jombart, Dr. Zhain Kamvar https://www.prstatistics.com/course/reproducible-data-science-for-population-genetics-rdpg02/ 10. 25th February – 1st March 2019 MOVEMENT ECOLOGY (MOVE02) Margam Discovery Centre, Wales, Dr. Luca Borger, Prof. Ronny Wilson, Dr Jonathan Potts https://www.prstatistics.com/course/movement-ecology-move02/ 11. March 4th – 8th 2019 BIOACOUSTICS FOR ECOLOGISTS: HARDWARE, SURVEY DESIGN AND DATA ANALYSIS (BIAC01) Glasgow, Scotland, Dr. Paul Howden-Leach https://www.prstatistics.com/course/bioacoustics-for-ecologists-hardware-survey-design-and-data-analysis-biac01/ 12. March 11th – 15th 2019 ECOLOGICAL NICHE MODELLING USING R (ENMR03) Glasgow, Scotland, Dr. Neftali Sillero http://www.prstatistics.com/course/ecological-niche-modelling-using-r-enmr03/ 13. March 18th – 22nd 2019 INTRODUCTION TO STATISTICS AND R FOR EVERYONE (IRFE01) Crete, GREECE, Dr Aristides (Aris) Moustakas https://www.prstatistics.com/course/introduction-to-statistics-and-r-for-anyone-irfe01/ 14. March 25th – 29th 2019 LANDSCAPE GENETIC DATA ANALYSIS USING R (LNDG03) Glasgow, Scotland, Prof. Rodney Dyer http://www.prstatistics.com/course/landscape-genetic-data-analysis-using-r-lndg03/ 15. April 1st – 5th 2019 INTRODUCTION TO STATISTICAL MODELLING FOR PSYCHOLOGISTS USING R (IPSY01) Glasgow, Scotland, Dr. Dale Barr, Dr Luc Bussierre http://www.psstatistics.com/course/introduction-to-statistics-using-r-for-psychologists-ipsy02/ 16. April 1st – 5th 2019 INDIVIDUAL BASED MODELS FOR ECOLOGSITS (IBME01) Glasgow, Scotland, Dr Aristides (Aris) Moustakas Link to follow 17. April 8th – 12th 2019 MACHINE LEARNING (MLUR01) Glasgow, Scotland, Dr Aristides (Aris) Moustakas https://www.prstatistics.com/course/machine-learning-using-r-mlur01/ 18. April 29th – May 3rd 2019 COMPARATIVE GENOMICS (CMGN01) Glasgow, Scotland, Dr. Fritz Sedlazeck, Dr. Matthias Weissensteiner https://www.prinformatics.com/course/comparative-genomics-cmgn01/ 19. May 6th – 10th 2019 NETWORK ANAYLSIS FOR ECOLOGISTS USING R (NTWA03) Myuna Bay, AUSTRALIA, Dr. Marco Scotti www.prstatistics.com/course/network-analysis-ecologists-ntwa03/ 20. May 16th – 18th 2019 (please note this a 3-day course from Thursday to Saturday) AQUATIC MOVEMENT ECOLOGY USING R (AMER01) Myuna Bay, AUSTRALIA, Dr. Ross Dwyer, Dr. Vinay Udyawer Link to follow 21. May 16th – 19th 2019 (please note this a 4-day course from Thursday to Monday) INTRODUCTION TO R FOR EVERYONE (IRFE02) Myuna Bay, AUSTRALIA, Dr Aristides (Aris) Moustakas https://www.prstatistics.com/course/introduction-to-statistics-and-r-for-anyone-irfe02/ 22. May 20th – 24th 2019 MODEL BASE MULTIVARIATE ANALYSIS OF ABUNDANCE DATA USING R (MBMV03) Myuna Bay, AUSTRALIA, Prof. David Warton https://www.prstatistics.com/course/model-based-multivariate-analysis-of-abundance-data-using-r-mbmv03/ 23. May 21st – 24th 2019 STATISTICAL TOOL BOX FOR ECOLOGISTS (TKFE01) Myuna Bay, AUSTRALIA, Dr Aristides (Aris) Moustakas https://www.prstatistics.com/course/statistical-toolkit-for-ecologists-tkfe01/ 24. June 10th – 14th 2019 STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR (SIMM04) Glasgow, Scotland, Dr. Andrew Parnell, Dr. Andrew Jackson www.prstatistics.com/course/stable-isotope-mixing-models-using-r-simm04/ 25. June 17th – 21st 2019 INTRODUCTION TO PYTHON FOR BIOLOGISTS (IPYB06) Glasgow, Scotland, Dr. Martin Jones http://www.prinformatics.com/course/introduction-to-python-for-biologists-ipyb06/ 26. June 24th – 28th 2019 ADVANCED PYTHON FOR BIOLOGISTS (APYB03) Glasgow, Scotland, Dr. Martin Jones www.prinformatics.com/course/advanced-python-biologists-apyb03/ 27. July 1st – 5th 2019 DATA VISUALISATION AND MANIPULATION USING PYTHON (DVMP01) Glasgow, Scotland, Dr. Martin Jones http://www.prinformatics.com/course/data-visualisation-and-manipulation-using-python-dvmp01/ 28. September 30th – October 4th 2019 GEOMETRIC MORPHOMETRICS USING R (GMMR02) Glasgow, Scotland, Prof. Dean Adams, Prof. Michael Collyer, Dr. Antigoni Kaliontzopoulou http://www.prstatistics.com/course/geometric-morphometrics-using-r-gmmr02/ 29. October 7th – 11th 2019 CONSERVATION PLANNING USING PRIORITIZR : FROM THEORY TO PRACTICE (PRTZ01) Crete, GREECE, Dr Richard Schuster and Nina Morell https://www.prstatistics.com/course/conservation-planning-using-prioritizr-from-theory-to-practice-prtz01/ 30. October 21st – 25th 2019 A COMPLETE GUIDE TO MIXED MODELS (INCLUDING TEMPORAL AND SPATIAL AUTOCORRELATION) (MMTS01) Crete, GREECE, Dr Aristides (Aris) Moustakas https://www.prstatistics.com/course/a-complete-guide-to-mixed-models-including-temporal-and-spatial-autocorrelation-mmts01/ Oliver Hooker PhD. PR informatics 2018 publications - Alternative routes to piscivory: Contrasting growth trajectories in brown trout (Salmo trutta) ecotypes exhibiting contrasting life history strategies. Ecology of Freshwater Fish. DOI to follow Phenotypic and resource use partitioning amongst sympatric lacustrine brown trout, Salmo trutta. Biological Journal of the Linnean Society. DOI 10.1093/biolinnean/bly032
