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227-0085-33L 3 Credits BSC D-ITET

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P&S: Accelerating Genome Analysis with FPGAs, GPUs, and New Execution Paradigms

Lecturers & Examiners: Dr. Can Firtina

The course unit can only be taken once. Repeated enrollment in a later semester is not creditable.

VVZ CR n/a

Last Updated: 2026-02-05 16:14:44

Abstract

The category of "Laboratory Courses, Projects, Seminars" includes courses and laboratories in various formats designed to impart practical knowledge and skills. Moreover, these classes encourage independent experimentation and design, allow for explorative learning and teach the methodology of project work.

Objective

Genome analysis is a cornerstone for groundbreaking scientific and medical advancements, including personalized healthcare. However, the field faces significant computational challenges, such as algorithmic bottlenecks and the handling of large datasets. This course aims to provide a comprehensive understanding of these computational facets, spanning across the computing stack from algorithms, software & tools, to microarchitecture & hardware accelerators. The course will cover how advanced hardware solutions like FPGAs and GPUs can expedite genome analysis by reducing computational time and energy consumption. In parallel, it will delve into the use and development of heuristic algorithms & tools for accelerating genome analysis across various computational platforms. These algorithms, for example, can offer tradeoffs between computational intensity and accuracy. Students will engage in hands-on projects focused on optimizing existing methods or innovating new solutions for genome analysis. The curriculum’s dual emphasis on hardware solutions and versatile algorithmic strategies offers students a holistic view of the current challenges and potential resolutions within the realm of genome analysis. The course is conducted in English. Course website: https://safari.ethz.ch/projects_and_seminars/doku.php?id=bioinformatics

Content

The students carry out a hands-on project under the supervision of their mentors. We also offer the following lectures that the students are encouraged to follow to make impactful progress on their projects. Lecture 1a: P&S Course Introduction & Scope Lecture 1b: Project Overview and Q&A Lecture 2: Introduction to Genome Analysis Lecture 3: From Molecules to Data: An Overview of DNA Sequencing Technologies Lecture 4a: Fundamentals of Sequence Alignment: Algorithms and Applications Lecture 4b: Optimizing Sequence Search: Hashing, Indexing, and Filtering Techniques Lecture 5a: Building the Blueprint of Life: Genome Assembly Lecture 5b: Generating Insights from Genome Analysis: Variant Calling and Functional Genomics Lecture 6a: GateKeeper Lecture 6b: SneakySnake Lecture 6c: GRIM-Filter Lecture 7a: GenASM Lecture 7b: Scrooge Lecture 8: SeGraM Lecture 9: GenStore Lecture 10a: GenPIP Lecture 10b: TargetCall Lecture 11a: BLEND Lecture 11b: AirLift Lecture 12a: Raw Nanopore Signal Analysis & RawHash

Resources

Lecture Notes

See:https://safari.ethz.ch/projects_and_seminars/doku.php?id=bioinformatics

Literature

Learning Materials =============== 1. Overview paper on co-designing hardware and software for genome analysis: https://people.inf.ethz.ch/omutlu/pub/AcceleratingGenomeAnalysis_dac23.pdf 2. Survey on the main steps in the genome analysis pipeline and their bottlenecks: https://people.inf.ethz.ch/omutlu/pub/IntelligentGenomeAnalysis_csbj22.pdf 3. Survey on accelerating genome analysis: https://people.inf.ethz.ch/omutlu/pub/AcceleratingGenomeAnalysis_ieeemicro20.pdf 4. Detailed survey on state-of-the-art algorithms for sequencing data: Link 5. Example of accelerating genomic sequence matching with FPGAs or GPUs: Link 6. Example using different computing paradigms for read mapping and alignment, improving energy consumption: https://arxiv.org/pdf/1711.01177.pdf , https://arxiv.org/pdf/2208.01243.pdf 7. Examples of software/hardware co-design for genomic sequence matching: - Link - Link - https://people.inf.ethz.ch/omutlu/pub/GenStore_asplos22-arxiv.pdf - https://arxiv.org/pdf/2209.08600.pdf 8. Example on analyzing raw nanopore signals: https://arxiv.org/pdf/2301.09200.pdf

General Information

Language: English
Levels: BSC
Frequency: Semesterly recurring

Examination

Type: ungraded semester performance

Registration & Places

Signup Start: 15.09.2023
Signup End: 29.09.2023

Course Components

Type	Title	Time & Place	Hours
practical/laboratory course	P&S: Accelerating Genome Analysis with FPGAs, GPUs, and New Execution Paradigms Für den Zugang zum Angebot und zur Einschreibung loggen Sie sich hier ein (mit Ihrem n.ETHZ account): Bitte beachten Sie, dass die Seite jeweils erst zwei Wochen vor Semesterbeginn zugänglich ist und im Verlauf des Semesters wieder abgeschaltet wird. Die Einschreibung ist nur von Freitag vor Semesterbeginn bis zum ersten Freitagmittag im Semester möglich. To access the offer and to enroll for courses log in (with your n.ethz account): Please note that the P&S-site is accessible no earlier than two weeks before the start of the semester until four weeks after the start of the semester. Enrollment is only possible from Friday before the start of the semester until noon of the first Friday in the semester. Time: to be arranged with each student Location: various	No time listed	3 h weekly

Offered In

Electrical Engineering and Information Technology Bachelor
- Laboratory Courses, Projects, Seminars (A minimum of 15 cp must be achieved in the category "Laboratory Courses, Projects, Seminars)
  - Projects & Seminars (Enrolment is only possible for students in the BSc Electrical Engineering and Information Technology from Friday before the start of the semester. Places are allocated using the P&S application tool ( ). Please only enrol for P&S for which you apply via the tool.)