Data preparation and quality assessment in genome assembly and annotation

- Wednesday, November 20, 2024, 1-4 pm CT
  - Lead: Genome Informatics Facility at Iowa State University
  - Prerequisites:
    - Familiarity with basic command-line concepts. We will offer virtual training for these skills before the Forum begins.
  - Data Prep Markdown File
  - Assembly and Assessment Markdown File
  - Genome Annotation Markdown File

In this workshop, participants will explore techniques for evaluating the accuracy and completeness of genome assemblies and annotations, helping attendees understand key metrics and statistical methods used to assess the quality of genomic data.

Knowing how to evaluate a genome will ensure reliable results for downstream, AI-based analyses like gene model prediction, variant detection, or comparative studies. Participants will also learn how to extract the transcripts and proteins from their genomes, to enable a variety of downstream AI-based applications, such as protein structure prediction. By the end of the workshop, attendees will be better equipped with the practical skills necessary to evaluate genomes and annotations for a range of bioinformatics applications.

Tutorial Setup Instructions

Steps to prepare for the tutorial session:

Login to Atlas Open OnDemand at https://atlas-ood.hpc.msstate.edu/. For more information on login procedures for web-based SCINet access, see the SCINet access user guide.
Open a command-line session by clicking on “Clusters” -> “Atlas Shell Access” on the top menu. This will open a new tab with a command-line session on Atlas’ login node.

Request resources on a compute node by running the following command:

 srun --reservation=forum -A scinet_workshop1 -t 00:30:00 -n 1 --mem 8G --pty bash 

Create a workshop working directory and copy the workshop materials into it by running the following commands. Note: you do not have to edit the commands with your username as it will be determined by the $USER variable.
```
 mkdir -p /90daydata/shared/$USER 
 cd /90daydata/shared/$USER 
 cp -r /project/ai_forum/assembly_prep . 
```
Stop the interactive job on the compute node by running the command exit.