Genome sequencing and metagenomics

Code:

BIOINF3001

Acronym:

BIOINF3001

Instance: 2025/2026 - 1S

Active?	Yes
Responsible unit:	Department of Biology
Course/CS Responsible:	Bachelor in Bioinformatics

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
L:BIOINF	21	Official Study Plan	3	-	6	48	162

Teaching language

Portuguese

Objectives

• 
  

  Expand knowledge on the structure of prokaryotic genomes, in articulation with the Microbiology course unit, acquiring fundamental concepts such as core genome, accessory genome, and pangenome.

  
  


• 
  

  Understand the relevance of genomics and metagenomics for the characterization of new prokaryotic species and for inferring microbial diversity in different environments.

  
  


• 
  

  Identify potential applications of genomics and metagenomics in both fundamental and applied research, with emphasis on biodiversity, biotechnology, and biomedicine.

  
  


• 
  

  Recognize and use the main genome and metagenome databases.

  
  


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  Become familiar with different second- and third-generation sequencing platforms, as well as methodologies associated with sample processing, sequencing, and bioinformatic analysis of genomes and metagenomes (quality control, assembly, data acquisition, and annotation against reference genomes).

  
  


• 
  

  Develop skills in comparative genomics, including synteny analyses and functional classification of genes.

  
  


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  Understand and apply the complete workflow for studying prokaryotic diversity in complex natural samples, including sample collection, eDNA isolation, sequencing using the MinION platform (Oxford Nanopore Technologies), and the bioinformatic analysis of the resulting data.

  
  

Learning outcomes and competences

• 
  

  Consolidate and expand knowledge on prokaryotic genome structure, building on concepts from the Microbiology course unit, and acquire new concepts in genomics, comparative genomics, and metagenomics.

  
  


• 
  

  Understand the advantages and limitations of major second- and third-generation sequencing technologies, including practical experience with sample processing and sequencing using the MinION platform (Oxford Nanopore Technologies).

  
  


• 
  

  Plan and implement genomics and metagenomics projects across all stages, from sample collection and eDNA isolation to data analysis, using available bioinformatics software and pipelines (e.g., tools hosted on GitHub).

  
  


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  Demonstrate a comprehensive understanding of bioinformatics solutions for genomic and metagenomic analyses, with particular focus on genome assembly, annotation, and comparative analyses.

  
  


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  Critically analyze case studies, collect relevant genomic and metagenomic data and metadata from public databases, and replicate published analyses, interpreting results in the context of scientific questions.

  
  


• 
  

  Apply a complete workflow for studying prokaryotic diversity in complex natural samples, integrating experimental and computational steps, from sample collection and eDNA isolation to sequencing and bioinformatic data analysis.

  
  

Working method

Presencial

Pre-requirements (prior knowledge) and co-requirements (common knowledge)

Basic knowledge of microbiology, molecular biology, and bioinformatics

Program

• Fundamentals of Genomics and Metagenomics: Essential concepts and applications in the study of microbial diversity and the discovery of new species.

• Sequencing Technologies: Analysis of 2nd-generation (short-read) and 3rd-generation (long-read) platforms, their advantages and limitations, and sample preparation methodologies.

• Practical Experience in Sequencing: Use of 3rd-generation platforms for real-time data generation.

• Genome Structure and Analysis: Study of the architecture of bacterial and archaeal genomes (core genome, accessory genome, and pangenome) and the use of genomic databases.

• Genomic Analysis Pipeline: Bioinformatics workflow for read processing, assembly, quality control, and automatic genome annotation.

• Comparative Genomics and Phylogenomics: Synteny analysis (BRIG), functional classification of genes, and application of ANI (Average Nucleotide Identity) for taxonomy and evolutionary studies.

• Metagenomics and Metabarcoding: Methodologies from sample collection (eDNA) and library preparation to diversity data analysis.

• Introduction to Transcriptomics: Concepts of gene expression analysis (RNA-seq) and its integration with genomic data for a functional perspective.

• Integrated Project and Case Study Analysis: Practical application of the full workflow in the study of a complex sample, replicating and interpreting results from scientific publications.

Mandatory literature

Pevsner, J. ; Bioinformatics and Functional Genomics. 3rd Edition. Wiley-Blackwell., 2015
Lesk, A. M.; Introduction to Bioinformatics. 5th Edition. Oxford University Press., 2019
Pierre Taberlet et al.; Environmental DNA for Biodiversity Research and Monitoring. Oxford Academic., 2018
Johannes B. Goll et al. ; Metagenomics and microbiomes in Bioinformatics and Data Analysis in Microbiology, Özlem Taştan Bishop, 2014
Ian L. Pepper, Charles P. Gerba, Terry J. Gentry. ; Environmental microbiology. 3rd ed . Amsterdam: Elsevier/AP, ISBN 978-0-12-394626-3, 2015

Teaching methods and learning activities

The course unit is organized into lectures, computational activities in the bioinformatics laboratory, and laboratory sessions, promoting discussion, problem-solving, and practical hands-on activities, and fostering strong interaction between instructors and students.

The laboratory sessions include sample processing, eDNA isolation, and sequencing, as well as the processing of reads from genome and metagenome sequences and the execution of bioinformatics routines for assembly and annotation of new genomic and metagenomic sequences, using source code and pipelines available on GitHub.

During the bioinformatics sessions, students also perform comparative genomics exercises, integrating and applying concepts acquired in the lectures and developing practical and analytical skills.

The course unit also includes individual and group projects, in which students apply the course content to real-world cases, promoting the practical application of theoretical knowledge and the development of research, critical analysis, and problem-solving skills.

When appropriate, learning may be reinforced through blended learning, using platforms such as Moodle, allowing students to enhance and consolidate knowledge acquired during contact hours and encouraging independent study.

Evaluation Type

Distributed evaluation with final exam

Assessment Components

designation	Weight (%)
Exame	50,00
Trabalho prático ou de projeto	50,00
Total:	100,00

Amount of time allocated to each course unit

designation	Time (hours)
Estudo autónomo	114,00
Frequência das aulas	48,00
Total:	162,00

Eligibility for exams

In accordance with Article 10 of the Assessment of Undergraduate Students at the University of Porto, approved by Rectoral Orders GR.02/05/2010 and GR.04/01/2017, it is established that, in order to obtain attendance credit for this course unit, a student must not exceed the maximum number of absences corresponding to 25% of the laboratory sessions.

Students covered by situations provided for by law are exempt from this requirement, without prejudice to the provisions of Article 11, paragraph 3 of the aforementioned regulation.

Assessment Method and Admission to the Final Exam

Assessment in this Course Unit is continuous with a final exam. Admission to the final exam requires the cumulative fulfillment of the following conditions:

a) Having obtained attendance in the Course Unit (as specified in the previous section).

b) Obtaining a minimum grade of 8.0 out of 20 in the practical assignments.

Failure to meet either condition (a) or (b) prevents the student from taking the final exam, resulting in failure due to missing assessment components.

Calculation formula of final grade

EX – Exam – 50% (10 points)
(Notes: exam covering theoretical content (70%) and practical content (30%))

VP – Completion of two practical assignments – 50% (10 points)
(Notes: group and/or individual assignments according to guidelines provided to students)

Final Grade = EX + VP

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For successful completion of the Course Unit, the student must simultaneously meet the following conditions:

a) Achieve a Final Grade (FG) equal to or greater than 10 points (on a 0–20 scale).

b) Obtain a minimum grade of 8 points (on a 0–20 scale) in the Exam.

Failure to achieve the minimum grade in any of the assessment components (practical work or exam) results in failure in the Course Unit, regardless of the calculated Final Grade.

Examinations or Special Assignments

This course unit does not include special exams and/or assignments.

Internship work/project

This course unit does not include internship project

Special assessment (TE, DA, ...)

Course unit without special assessment

Classification improvement

Only the assessment component related to the Exam (50%) is eligible for grade improvement.

Observations

Course unit jury: Catarina Magalhães (regente), Nuno Fonseca (regente), Fernando Tavares.