3  Day 2 - Bioinformatics Session

Metagenome Analysis and Phage Mining

Published

October 16, 2025

Topic Description Date Venue
Bioinformatics Session: Manage and Analyze Metagenomics Data Accessing and utilizing the KBase Platform. Perform QC, Assembly, Binning, and Automation of Metagenomics Datasets. Use various bioinformatics tools for phage Mining. Thursday, 16 October 2025 Teaching Lab, Building B, Second Floor, Faculty of Biology UGM

3.1 Programme Description and Schedule

The second day shifts from wet-lab work to data analysis, focusing on metagenome analysis and phage mining led by Bent Petersen from the Center for Evolutionary Hologenomics, University of Copenhagen. The morning session will introduce participants to metagenomic workflows using KBase, covering quality control, assembly, and binning. In the afternoon, participants will explore phage detection and characterization using advanced tools developed by the Center for Evolutionary Hologenomics, gaining hands-on experience in uncovering microbial and viral diversity from metagenomic datasets.

ImportantWorkshop Materials

All datasets and analyses for this session are available in the official KBase Narrative prepared by Bent Petersen:
➡️ https://narrative.kbase.us/narrative/ws.230917.obj.42

Please sign in to KBase before the session so you can access and duplicate the workflow.

WarningBefore You Begin – Copy the Narrative

The shared KBase Narrative is read-only, meaning you can explore all completed steps and results but cannot run new analyses within it.
To perform your own analyses during the workshop:

  1. Open the Narrative:
    🔗 https://narrative.kbase.us/narrative/ws.230917.obj.42
  2. In the left corner, click Narratives.
  3. Select “Copy this Narrative” to create your own editable version in your KBase account.
  4. Your copy will include all apps and inputs but no finished jobs, so you can start each step from scratch.

Tip: Rename your narrative (e.g., “My_ICBS_Workshop_Analysis”) so you can easily find it later.

TipWorkshop Presentations

NOTE: The password for the presentations is: phagesarecool 1 Presentation: Pre-processing of NGS Data
2 Presentation: De novo Assembly – Piecing Together Genomes
3 Presentation: PhageCompass - Publicly available tools to support the therapeutic use of phages

Time Session Speaker/Facilitator
07:30 – 08:00 Registration
08:00 – 08:15 Opening & Recap of Day 1 Workshop Chair
08:15 – 09:30 Lecture: Introduction to Metagenome Analysis Bent Petersen
09:15 – 09:30 Coffee Break
09:45 – 11:30 Hands‑on Practical I: Metagenome Analysis Pipeline (QC → Assembly → Binning) Bent Petersen
11:30 – 12:15 Discussion / Troubleshooting Bent Petersen
12:15 – 13:15 Lunch Break
13:15 – 14:00 Lecture: Phages in Metagenomes – Concepts & Tools Bent Petersen
14:00 – 15:00 Hands‑on Practical II: Phage Mining from Metagenome Data Bent Petersen
15:00 – 15:30 Wrap‑up Discussion Workshop Chair

3.2 Instructors & Facilitators

Bent Petersen, PhD
Center for Evolutionary Hologenomics, University of Copenhagen

Adhisa F. Putri, S.Si.
Bioinformatician
Integrated Genome Factory

Fahrunnida, MMolBio
Research Assistant
Faculty of Biology UGM

Lucia Arum Sekar Meysari, S.Si.
Student
Faculty of Biology UGM

Muhammad Ridwan Adyatama
Student
Faculty of Pharmacy UGM

3.3 Participant list

No. Name Institution
1 Nauval Rajwaa R Universitas Gadjah Mada
2 I Gusti Agung Ayu Ratna Puspitasari Universitas Jenderal Soedirman
3 Gres Maretta Universitas Gadjah Mada
4 Rinanti Eka Aldis Universitas Gadjah Mada
5 Periskila Dina Kali Kulla Universitas Gadjah Mada
6 Kurniawan Universitas Gadjah Mada
7 Zahrotin Saleha Universitas Gadjah Mada
8 Anggun Diyan Nurhasanah Universitas Gadjah Mada
9 Irma Kresnawati Indonesia Oil Palm Research Institute
10 Nafi’ah Khoirunnisa’ Universitas Gadjah Mada
11 Chrisnanda Ayu Melati Universitas Gadjah Mada
12 Aisyah Riziq Rohmah Universitas Gadjah Mada
13 Aulia Robiatul Adawiyah Universitas Gadjah Mada
14 Yunita Messe Universitas Gadjah Mada
15 Rohmi Salamah Universitas Gadjah Mada
16 Luh Putu Ayu Dini Kristina Puspitadewi biou
17 Bihar Hikam Ahmadi biou
18 Siti Fatimah Sabran UTHM, Malaysia
19 Nor Atiqah binti Norazlimi UTHM, Malaysia

3.4 What to Bring

Please come prepared to participate actively in the hands-on bioinformatics sessions.
All participants should bring:

  • A laptop computer (Windows, macOS, or Linux) with:
    • A modern web browser (Google Chrome or Firefox recommended)
    • A stable internet connection (Wi-Fi will be provided)
  • Charger / power adapter (the sessions are full-day; power outlets will be available)
  • Student/staff ID for on-site registration
  • Notebook or digital notes app for jotting down workflows and login information

Note: Please ensure your laptop can connect to external Wi-Fi networks (no firewall restrictions). The KBase and PhageCompass platforms are web-based and require online access throughout the session.

3.5 Pre-Event Preparation

Before attending the workshop, please complete the following steps to ensure a smooth and productive experience:

3.5.1 Create a KBase Account

We will perform all metagenome analyses using the KBase platform.
To participate, please create a free account before the workshop:

  1. Visit the KBase Getting Started page.
  2. Choose “Sign Up” using one of the supported identity providers:
    • Google
    • ORCiD
    • Globus
  3. Once your sign-in is established, you can access the KBase Narrative Interface to begin your analyses.

Reference:
KBase Step-by-Step Signup Guide →

3.5.2 Familiarize Yourself with the KBase Metagenomics Tutorial

We will follow the official Metagenomic & Community Analysis workflow in KBase: > “Running Metagenomic and Community Analysis in KBase”

This tutorial introduces essential steps for microbial community analysis using real metagenomic reads, including: - Quality control (FastQC, trimming) - Assembly and binning - Genome annotation (Prokka) - Exploration of metabolic potential and taxonomic diversity

Tutorial reference: KBase Metagenomic & Community Analysis

3.5.3 Review the Workshop Narrative (Tara Oceans Dataset)

Our session will use a pre-assembled KBase Narrative prepared by Bent Petersen, available at:

🔗 https://narrative.kbase.us/narrative/230597

This narrative begins with raw reads, performing: - Quality control (FastQC & trimming)
- Assembly and filtering by contig length
- Annotation with Prokka

Because the original dataset is large, Bent has prepared a subsampled version to make the workflow faster during the workshop.
You will also be able to export assembled contigs and explore downstream tools at PhageCompass.dk.

3.5.4 Explore Phage Tools (Optional Pre-Read)

We will use several tools from the PhageCompass platform to study viral diversity and phage genomics:

  • Phager (in development)
  • PhageLeads – host range prediction
  • TaxMyPhage – taxonomic classification of phages
  • PhageClouds – comparative visualization of phage populations

If you have time before the workshop, explore the PhageCompass portal and familiarize yourself with its interface and example datasets.

Completing the above steps will ensure you’re ready to dive directly into the analyses on Day 2 without setup delays.
Please contact the workshop team if you face login or access issues prior to the event.