Abstract Detail

Conference Wide

Landis, Jacob [1], Li, Fay-Wei [2], Strickler, Susan [3], Powell, Adrian [4].

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

The costs of generating a draft genome for a study organism of choice are declining each year and more tools are becoming available to help in the endeavor. However, generating the appropriate sequence data is often not a trivial matter and currently, there are many options when it comes to analysis pipelines. 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 and baseline skills: ● Unix command-line skills (http://swcarpentry.github.io/shell-novice/) ● Familiarly with some basic programming (http://swcarpentry.github.io/python-novice-inflammation/; http://swcarpentry.github.io/r-novice-inflammation/) ● CyVerse account (https://user.cyverse.org/) ● XSEDE account (https://portal.xsede.org/allocations/education) Topics ● Introduction to genome sequencing and assembly ● Setting hardware/software baseline skills ● Generating suitable DNA for different platforms: tips, tricks, and experimental design ● Sequencing data and genome assembly options ● Genome annotation ● Downstream evolution analyses: genome management, genome visualization, comparative genomics, reference-based SNP calling, transcriptomics, and phylogenomics ● Consulting Services

1 - Cornell University
2 - Boyce Thompson Institute, 105 Valley Road, Ithaca, NY, 14850, United States
3 - Boyce Thompson Institute For Plant Research , 533 Tower Road, Ithaca, NY, 14853, United States
4 - Boyce Thompson Institute

Keywords:
none specified

Presentation Type: Workshop
Number: W06001
Abstract ID:20
Candidate for Awards:None