De novo genome assembly and annotation with an emphasis on phylogenetic and population genetic studies

Registration is now open for the BCBC’s workshop on De novo genome assembly and annotation with an emphasis on phylogenetic and population genetic studies. The workshop is planned for May 4, 2021, from 9am to 5:15pm.

Please register for the workshop here. Attendance will be limited to 20 participants. Participation in this instance of the workshop will be free of charge.

The focus of this workshop is to work through the necessary steps for genome assembly and annotation when a closely related reference genome is not available. The workshop will cover assembling genomes using Illumina, Oxford Nanopore, and hybrid assemblers; as well as methods for extracting high-quality DNA suitable for ONT sequencing and library preparation, especially in species that possess secondary compounds which can be especially problematic for nanopore sequencing. Downstream applications/analyses that can be performed after assembly will also be covered while highlighting that a perfect assembly is not necessary to answer many evolutionary questions. Using the CyVerse platform, participants will get hands-on practice with all the necessary steps using either the supplied test data or their own data if previously generated.

Prerequisites
-Basic Unix/Linux command-line skills (as covered in sessions 1 and 2 of the BCBC Intro. to Bioinformatics Course or other similar resources). If you have not attended the Intro. to Bioinformatics Course, resources and materials for these sessions are available on the course website.

Topics
-Introduction to genome sequencing and assembly (Susan Strickler)
-Setting hardware/software baseline skills (Adrian Powell)
-Generating suitable DNA for different platforms: tips, tricks, and experimental design (Fay-Wei Li)
-Sequencing data and genome assembly options (Jacob Landis)
-Genome annotation (Susan Strickler)
-Downstream evolution analyses: genome management, genome visualization, comparative genomics, reference-based SNP calling, transcriptomics, and phylogenomics (Andrew Nelson, Adrian Powell)