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DTSTART;TZID=Europe/Stockholm:20231106T090000
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DTSTAMP:20260403T205030
CREATED:20230818T135627Z
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UID:155646-1699261200-1699635600@www.scilifelab.se
SUMMARY:DDLS Population genomics in practice
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of hands-on and practical skills for the analyses of population genomics data. \n\n\n\n\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2023-08-17 \n\n\n\nApplication closes: 2023-09-30 \n\n\n\nConfirmation to accepted students: 2023-10-10 \n\n\n\nCourse Leader and teachers: Per Unneberg (CL)\, Nikolay Oskolkov\, Jason Hill\, André Soares \n\n\n\nIn case you miss information on any of the above dates\, please contact: edu.population-genomics-in-practice@nbis.se \n\n\n\n\n\n\n\nCourse fee\n\n\n\nA course fee* of 3000 SEK will be invoiced to accepted participants. The fee includes lunches\, coffee and snacks. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse Website\n\n\n\n\n\n\n\n\n\nCourse content\n\n\n\nThe aim of this workshop is to provide an introduction to commonly used methods in population genomics. As the focus of the course is on hands-on work\, the topics have been designed to cover the fundamental analyses that are common in many population genomics studies. The course consists of lectures and exercises\, with a focus on the practical aspects of analyses. Whereas lectures introduce some background theory\, their primary aim is to set the stage for accompanying exercises. \n\n\n\nTopics covered will include: \n\n\n\n\nFoundations of population genetics\n\n\n\nIntroduction to simulation and the coalescent\n\n\n\nBasics of variant calling\n\n\n\nVariant filtering and sequence masks\n\n\n\nCharacterization and interpretation of DNA sequence variation\n\n\n\nCalculation and interpretation of summary statistics from variation data\n\n\n\nInvestigating population structure with admixture modelling and principal component analyses\n\n\n\nDemographic modelling using sequentially Markovian coalescent models and linkage disequilibrium\n\n\n\nSelection scans\n\n\n\n\n\n\n\n\nLearning Outcomes\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\ndescribe the different forces of evolution and how they influence genetic variation\n\n\n\nunderstand and interpret genealogical trees and how they relate to genetic variation data\n\n\n\ndescribe the basics of the coalescent\n\n\n\nperform simple coalescent simulations with msprime\n\n\n\nrun simple SLiM forward simulation models\n\n\n\ndescribe and run the steps of a variant calling pipeline\, including quality control of raw reads\, read mapping\, and variant calling\n\n\n\nknow how and when to filter raw variant calls using manual coverage filters\n\n\n\ndescribe and calculate nucleotide diversity from variation data\n\n\n\nanalyse population structure with admixture modelling and dimensionality reduction methods\n\n\n\nperform demographic modelling with sequential Markovian coalescent models\n\n\n\ndescribe methods that identify regions undergoing adaptation and selection\n\n\n\nrun selection scans\, score identified regions and interpret findings in the context of genome annotations\n\n\n\n\n\n\n\n\n\n\nEntry Requirements\n\n\n\nThe following is a list of skills required for being able to follow the course and complete the exercises: \n\n\n\n\nBasic knowledge in R or Python\n\n\n\nBasic knowledge of variant calling\, or the equivalent of NBIS course “Introduction to Bioinformatics using NGS data”\n\n\n\nBasic knowledge of population genetics\n\n\n\nBasic understanding of frequentist statistics\n\n\n\nA computer\n\n\n\n\nDesirable\, but not essential\, skills increasing the output of the course\, include: \n\n\n\n\nExperience with analysis of NGS and other omic data\n\n\n\n\nDue to limited space the course can accommodate a maximum of 25 participants. If we receive more applications\, participants will be selected based on selection criteria\, including (but not limited to) correct entry requirements\, motivation to attend the course\, as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/population-genomics-in-practice/
LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
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