Introduction to genomic data analysis: from raw data to variant discovery

Advances in sequencing technology have made high-throughput data widely accessible, facilitating genomic research in non-model species. This course introduces the bioinformatics principles and practical skills required to analyse whole-genome sequencing data, from raw reads to variant discovery. Beginning with Linux and command-line fundamentals, participants will learn to acquire sequencing data, perform quality control and cleaning, align reads, process alignments, and identify and filter variants. Theoretical sessions and practical exercises will guide participants through each stage of the pipeline, concluding with an exploration of how different filtering approaches influence downstream analyses.

Linux and Bash fundamentals, file navigation and manipulation, pipes, loops, and basic scripting. Practical exercises will include managing files, processing multiple datasets, and setting up software with Conda.

Overview of sequencing technologies and acquisition of data from public repositories. Introduction to FASTQ/FASTA formats, followed by practical exercises in read quality assessment, adapter removal, trimming, and interpretation of quality reports.

Reference genome selection and preparation, alignment principles, and SAM/BAM formats. Practical exercises will cover read alignment, sorting, duplicate handling, and assessment of mapping and coverage statistics.

Introduction to variant calling, base quality score recalibration, and VCF/BCF formats. Practical exercises will cover variant detection and filtering using BCFtools, GATK, and PLINK2, including filters relevant to downstream analyses.

Comparison of filtering strategies applied to the same dataset and their effects on population genetic analyses.

5 days - 27 hours - Schedule: 09:30 - 12:30 & 14:00 - 17:00 (Friday only in the morning)

Coordination

Diana Lobo | BIOPOLIS-CIBIO

Arkadiusz Dziech | Wrocław University of Environmental and Life Sciences, Department of Genetics

Rita Gomes Rocha | BIOPOLIS-CIBIO

Instructor

Diogo Lima | BIOPOLIS-CIBIO

The course will be open to a maximum number of 20 participants.

60% of available student slots are reserved for BIODIV students.

Priority will be given to:

• 1st year and other PhD students attending the BIODIV Doctoral Program;

• PhD students attending other courses;

• Other post-graduate students, researchers and technical staff.

(A minimum number of participants is required for the course to take place)

Official applications for this course will be managed directly by FCUP. Detailed information will be available soon.

If you would like to be notified as soon as registrations open, please let us know by filling out our short form: Express Your Interest Here

⚠️ Please note: This form is not an official application. It simply allows us to keep you updated and helps us gauge the level of interest for each course.

No ECTS credits are awarded for attending the course. Participants receive a certificate of attendance without quantitative evaluation.

Education & Training Unit (Post graduation office)

+351 252 660 425