Project Resource

Pathways Project: Annotation Notebook

The Pathways Annotation Notebook will help GEP students keep track of their work as they are annotating, and then they can use the notebook to fill out the report form. This notebook does not have to be submitted to GEP, it’s just an extra resource students might find helpful.

Pathways Project: Annotation Report

GEP students will use the Report Form document to submit their annotation results for the Pathways Project. The Project Details Table handout will show students how to fill out the first page of the Annotation Report. The Report Form Exemplar is provided as an example of a completed report. The Annotation Workflow is a one page summary of the annotation protocol.  

Common Finishing Errors

This PowerPoint presentation describes the common errors observed in student finishing projects.

Finishing Checklist

Students should complete all items on this checklist before submitting the project back to the GEP.

Strategies for Finishing Hybrid Assemblies

This document contains advice on the strategies students can use to resolve common problems they may encounter during sequence improvement.

Calling Additional Reads

Students will typically need to request additional sequencing reactions in order to improve the quality of an assembly. This document describes some of the key considerations that students should keep in mind when they design oligonucleotide primers.

PCR Primer Selection Guide

This document contains advice on the factors that students should consider when designing PCR primers to resolve gaps and low quality regions. The document also includes the specific search parameters students should use to minimize the chance of off-target priming when designing PCR primers.

GEP Digital Laboratory Notebook

Developed by Dr. Nick Reeves at Mt. San Jacinto College, Menifee Valley Campus, this PowerPoint presentation provides a brief overview of the Digital Lab Notebook, which provides detailed guidance to students on the GEP annotation strategy.