Week 1: Intro to the course, omics data, and OSC

Author
Affiliation

Jelmer Poelstra

CFAES Bioinformatics Core, Ohio State University

Published

August 22, 2025


Overview

Welcome to the AU25 course Practical Computing Skills for Omics Data! In this first week of the course, you will get an overview of the course’s contents and introductions to omics data and the Ohio Supercomputer Center (OSC).

Learning goals & lectures

In each of the following lectures, you will learn:

Course intro (Tuesday class)

  • What to expect from this course
  • Which tools and languages we will use
  • What is expected of you during this course

Omics data (Tuesday/Thursday class)

  • What omics data is
  • What the main high-throughput sequencing technologies are
  • How Illumina sequence libraries are structured
  • What reference genomes are, and what they are good for
  • What the main sequence file types are and what FASTA, FASTQ, and GFF/GTF files look like

The Ohio Supercomputer Center (OSC) (Thursday class)

  • What a supercomputer is, and why they are useful
  • What resources the Ohio Supercomputer Center (OSC) provides
  • How to access OSC resources through its OnDemand webportal

Readings

  • Poinsignon et al. (2023): Working with omics data: An interdisciplinary challenge at the crossroads of biology and computer science
    This book chapter provides an overview of different kinds of omics data.

  • Markowetz (2015): Five selfish reasons to work reproducibly
    This short paper gives a light-hearted overview of self-interested reasons to perform your research reproducibly.

  • “Overview of Illumina Sequencing by Synthesis Workflow”
    Watch this 5-minute video to learn how Illumina sequencing works. This is meant to provide a bit more background, given that the example data in this course will be from Illumina sequencing. This is a very quick overview and you don’t need to understand all the details! (Optionally, also watch the video overviews of Oxford Nanopore and Pacific Biosciences sequencing technology that are embedded in the next two slides.)

Assignments & exercises

Further resources

Throughout the course, chapters from these two books are optional readings for this course. Both can be accessed online for free with OSU credentials via the links below.

Browse through the below paper titles and see if any of these spark your interest — many of these present omics and HTS data in a more field-specific light, e.g. plant pathology.

  • Lee (2023): The principles and applications of high-throughput sequencing technologies (link)
  • Dijk et al. (2023): Genomics in the long-read sequencing era (link)
  • Heyden et al. (2025): Advancing species conservation and management through omics tools (link)
  • Nizamani et al. (2023): High-throughput sequencing in plant disease management: a comprehensive review of benefits, challenges, and future perspectives (link)
  • Aragona et al. (2022): New-generation sequencing technology in diagnosis of fungal plant pathogens: A dream comes true? (link)
  • Mahmood et al. (2022): Multi-omics revolution to promote plant breeding efficiency (link)
  • Rai, Yamazaki, and Saito (2019): A new era in plant functional genomics (link)
  • Pinto and Bhatt (2024): Sequencing-based analysis of microbiomes (link)
  • Manzoni et al. (2018): Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences (link)
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References

Allesina, Stefano. 2019. Computing Skills for Biologists: A Toolbox. Princeton, NJ: Princeton University Press,. https://doi.org/10.1515/9780691183961.
Aragona, Maria, Anita Haegi, Maria Teresa Valente, Luca Riccioni, Laura Orzali, Salvatore Vitale, Laura Luongo, and Alessandro Infantino. 2022. “New-Generation Sequencing Technology in Diagnosis of Fungal Plant Pathogens: A Dream Comes True?” Journal of Fungi 8 (7): 737. https://doi.org/10.3390/jof8070737.
Buffalo, Vince. 2015. Bioinformatics Data Skills [Reproducible and Robust Research With Open Source Tools]. First edition. Beijing: O’Reilly.
Dijk, Erwin L. van, Delphine Naquin, Kévin Gorrichon, Yan Jaszczyszyn, Rania Ouazahrou, Claude Thermes, and Céline Hernandez. 2023. “Genomics in the Long-Read Sequencing Era.” Trends in Genetics 39 (9): 649–71. https://doi.org/10.1016/j.tig.2023.04.006.
Heyden, Sophie von der, Luciano B. Beheregaray, Sarah Fitzpatrick, Catherine E. Grueber, Yibo Hu, and Alison G. Nazareno. 2025. “Advancing Species Conservation and Management Through Omics Tools.” Molecular Ecology Resources 25 (5): e14123. https://doi.org/10.1111/1755-0998.14123.
Lee, Jun-Yeong. 2023. “The Principles and Applications of High-Throughput Sequencing Technologies.” Development & Reproduction 27 (1): 9–24. https://doi.org/10.12717/DR.2023.27.1.9.
Mahmood, Umer, Xiaodong Li, Yonghai Fan, Wei Chang, Yue Niu, Jiana Li, Cunmin Qu, and Kun Lu. 2022. “Multi-Omics Revolution to Promote Plant Breeding Efficiency.” Frontiers in Plant Science 13 (December). https://doi.org/10.3389/fpls.2022.1062952.
Manzoni, Claudia, Demis A Kia, Jana Vandrovcova, John Hardy, Nicholas W Wood, Patrick A Lewis, and Raffaele Ferrari. 2018. “Genome, Transcriptome and Proteome: The Rise of Omics Data and Their Integration in Biomedical Sciences.” Briefings in Bioinformatics 19 (2): 286–302. https://doi.org/10.1093/bib/bbw114.
Markowetz, Florian. 2015. “Five Selfish Reasons to Work Reproducibly.” Genome Biology 16 (1): 1–4. https://doi.org/10.1186/s13059-015-0850-7.
Nizamani, Mir Muhammad, Qian Zhang, Ghulam Muhae-Ud-Din, and Yong Wang. 2023. “High-Throughput Sequencing in Plant Disease Management: A Comprehensive Review of Benefits, Challenges, and Future Perspectives.” Phytopathology Research 5 (1): 44. https://doi.org/10.1186/s42483-023-00199-5.
Pinto, Yishay, and Ami S. Bhatt. 2024. “Sequencing-Based Analysis of Microbiomes.” Nature Reviews Genetics 25 (12): 829–45. https://doi.org/10.1038/s41576-024-00746-6.
Poinsignon, Thibault, Pierre Poulain, Mélina Gallopin, and Gaëlle Lelandais. 2023. “Working with Omics Data: An Interdisciplinary Challenge at the Crossroads of Biology and Computer Science.” In, 313–30. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3195-9_10.
Rai, Amit, Mami Yamazaki, and Kazuki Saito. 2019. “A New Era in Plant Functional Genomics.” Current Opinion in Systems Biology, Gene regulation, 15 (June): 58–67. https://doi.org/10.1016/j.coisb.2019.03.005.