ANNOUNCEMENT CPANG18 Computational PANgenomics with Tobias Marschall and Erik Garrison The GTPB is proud to announce that the above referenced hands-on training course is open for applications IMPORTANT DATES for this Course Deadline for applications: February 23rd 2018 Course date: March 6th - March 9th 2018 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Course Description Reference genomes have become central to bioinformatics approaches, and form the core of standard analyses using contemporary sequencing data. However, the use of linear reference genomes, which provide the sequence of one representative genome for a species, is increasingly becoming a limitation as the number of sequenced genomes grows. In particular, they tend to bias us away from the observation of variation in the genomes we study. A general solution to this problem is to use a pangenome that incorporates both sequence and variation from many individuals as our reference system. This pangenome is naturally modeled as a graph with annotations, and can provide all the functionality traditionally provided by linear reference genomes. Unlike linear reference genomes, a pangenome readily incorporates both small and large variation, allowing bias-free genotyping at known alleles. In this course we will explore the use of modern bioinformatic tools that allow researchers to use pangenomes as their reference system when engaging in studies of organisms of all types. Such techniques will aid any researcher working on organisms of high genetic diversity or on organisms lacking a high-quality reference genome. This course targets all researchers interested in learning about an exciting paradigm shift in computational genomics. Objectives Participants first will learn about limitations of linear reference-based methods and work through 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 sources to develop an intuition about pangenomic methods and a practical familiarity with applicable tools. More information, and access to the application process here: http://gtpb.igc.gulbenkian.pt/bicourses/2018/PANG18 Ref: Computational pan-genomics: status, promises and challenges The Computational Pan-Genomics Consortium Author Notes Briefings in Bioinformatics, Volume 19, Issue 1, 1 January 2018, Pages 118–135, https://doi.org/10.1093/bib/bbw089 (OPEN ACCESS) Hoping that this course meets your interests, Pedro Fernandes -- Pedro L Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt -- The Gulbenkian Training Programme in Bioinformatics General Office Rua da Quinta Grande, 6 2780-156 OEIRAS Portugal _______________________________________________ GTPB mailing list GTPB@igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb