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DTSTAMP:20260808T230106Z
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DTSTART:20190909T090000Z
DTEND:20190913T170000Z
DESCRIPTION:Reference genomes have become central to bioinformatics approac
 hes\, and form the core of standard analyses using contemporary sequencing
  data. However\, the use of linear reference genomes\, which provide the s
 equence of one representative genome for a species\, is increasingly becom
 ing a limitation as the number of sequenced genomes grows. In particular\,
  they tend to bias us away from the observation of variation in the genome
 s we study. \n\nA general solution to this problem is to use a pangenome t
 hat incorporates both sequence and variation from many individuals as our 
 reference system. This pangenome is naturally modelled as a graph with ann
 otations and can provide all the functionality traditionally provided by l
 inear reference genomes. Unlike linear reference genomes\, a pangenome rea
 dily incorporates both small and large variation\, allowing bias-free geno
 typing at known alleles.\n\nIn this course we will explore the use of mode
 rn bioinformatic tools that allow researchers to use pangenomes as their r
 eference system when engaging in studies of organisms of all types. Such t
 echniques will aid any researcher working on organisms of high genetic div
 ersity or on organisms lacking a high-quality reference genome. This cours
 e targets all researchers interested in learning about an exciting paradig
 m shift in computational genomics.\n\nObjectives\n\nParticipants first wil
 l learn about limitations of linear reference-based methods and work throu
 gh a brief refresher or introduction to standard approaches for processing
  sequencing data\, including read alignment and variant calling. Provided 
 these motivating examples\, we will use data from a variety of relevant so
 urces to develop an intuition about pangenomic methods and a practical fam
 iliarity with applicable tools.
SUMMARY:CPANG19 
URL;VALUE=URI:http://gtpb.igc.gulbenkian.pt/bicourses/2019/CPANG19/
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