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Pathways Project: Annotation Workflow

  • November 13, 2020August 11, 2021

The Annotation Workflow is a one page summary of the annotation protocol for the Pathways Project. This workflow provides an overview of the key analysis steps and bioinformatics tools for the annotation of a putative ortholog.

Pathways Project: Annotation Notebook

  • September 14, 2020August 31, 2021

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.

Common Finishing Errors

  • August 15, 2020August 19, 2020

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

A Complex Drosophila Fosmid

  • August 15, 2020August 19, 2020

This fosmid from Drosophila virilis assembles into three contigs (a yellow clone). In this exercise, students must generate a final assembly by closing a gap, dealing with a mis-assembly, and improving low quality regions. Snapshots of the different stages of the assembly are stored as separate ace files.

A Simple Drosophila Fosmid

  • August 15, 2020August 19, 2020

This fosmid from Drosophila virilis assembles into a single contig (a green clone). In this exercise, students will need to identify regions in the assembly where additional data is needed and design additional sequencing reactions to bring the contig up to quality standards.

The D. grimshawi dot chromosome

  • August 15, 2020June 3, 2022

This PowerPoint presentation explains our strategy, detailing the source of the raw sequence data for the D. grimshawi dot chromosome.

Workflow to Resolve Misassembly

  • August 15, 2020August 19, 2020

A flowchart that illustrates the key decisions and strategies when dealing with misassemblies that are caused by collapsed repeats.