Overview

Teaching: 120 min
Exercises: 180 min

Objectives

• Read the abstract and introduction of the geNomad paper and extract the problem the tool was built to solve

• Follow and reconstruct how geNomad classifies a sequence

• Explain the tool in your own words, in writing

Reading a Tool Paper: geNomad

Every tool you run in this course makes decisions about your sequences. If you cannot describe those decisions, you cannot interpret the output, defend it in a discussion, or notice when it goes wrong. Today we want to understand something about virus identification. How can we do that only based on the assembled contigs we have now? In this theoretical part, we will try to make reading a tool paper closely enough to understand what the tool actually does a bit more fun by doing it together at the smart board.

Today we will read the paper: “Identification of mobile genetic elements with geNomad” (Camargo et al., 2023). geNomad identifies viruses and plasmids in sequencing data, assigns taxonomy to the viruses it finds, and annotates their genes. And it does this by combining two rather different ideas about what makes a sequence “viral”.

The session has three parts:

1. Read on your own. Read the abstract and the introduction.
2. Work through it together. We will then reconstruct how geNomad works at the board, step by step, until everyone feel like they can explain how the tool works in half a page.
3. Write it down. Half a page.

Questions to read with

1. What problem do the authors say existing tools have? What is geNomad supposed to do better, and for whom?

2. geNomad identifies mobile genetic elements, not only viruses. What are mobile genetic elements, and why might it make sense to look for viruses and plasmids with the same tool?

3. The abstract mentions two very different sources of information used for classification. What are they? What kind of signal does each one capture, and where do you expect each to fail?

4. Note down terms and concepts in the abstract and introduction that are new to you.

Write-up

After the board session, write about half (!) a page covering:

• How geNomad decides whether a sequence is a virus, a plasmid, or neither.
• What you learned, things you didn’t know before.
• One thing you still do not understand.

Have fun :)

Key Points

• geNomad combines two independent branches: an alignment-free model that reads the nucleotide sequence directly, and a gene-based model that uses marker protein profiles

• Going through a paper together at the board is fun. Jeroen is amazing at drawing :)