Learner Profiles

Graduate Student with a New Genome Assembly

---

Alex is a second-year PhD student in plant biology who has just received a chromosome-level genome assembly for a non-model legume species. Alex has basic command-line experience from a previous bioinformatics course and can navigate the HPC cluster, but has never performed genome annotation. Alex needs to annotate the genome to identify protein-coding genes for a comparative genomics study and wants to understand which annotation tool best fits the available RNA-seq data from three tissue types.

Postdoc Comparing Annotation Pipelines

---

Jordan is a postdoctoral researcher studying gene regulation in a crop species. Jordan has used MAKER for annotation before but wants to compare newer tools (BRAKER3, Helixer, EASEL) to determine which produces the most complete and accurate gene set. Jordan is comfortable with bash scripting and SLURM job submission but needs guidance on setting up the specific tools and interpreting quality metrics like BUSCO and OMArk scores.

Core Facility Bioinformatician

---

Sam works at a university genomics core facility and regularly receives requests to annotate genomes for researchers across departments. Sam has strong computational skills and needs to establish a standardized, reproducible annotation workflow that can be applied across diverse eukaryotic organisms. Sam is particularly interested in the functional annotation step with EnTAP and wants to document the pipeline for other facility staff.