SeqAn3 – a modern C++ library for efficient sequence analysis - GCB 2019
Start: Monday, 16 September 2019 @ 09:00
End: Monday, 16 September 2019 @ 17:00
• René Rahn (CIBI)
• GCB 2019, Heidelberg
Technological advances in sequencing and computer science have made it possible to generate enormous volumes of data in continuously decreasing time intervals, demanding highly efficient and fast algorithms and intelligent data structures for their analysis. However, implementation and maintenance of these is difficult, and thus can become a critical bottleneck for the time cost-effectiveness of many research projects.
To counter this gap, we develop SeqAn a general purpose and generic C++ software library, whose focus lies on sequence analysis. SeqAn contains a wide range of accelerated and most competitive algorithms, data structures and file formats. Recently, we started with SeqAn3 a major redesign of the API, based on bleeding-edge features from C++ ≥ 17/20. The goal of this endeavour is to simplify the programming interface to provide an easy access to complex and system dependent algorithms and data structures.
In this de.NBI/ELIXIR hands-on tutorial, we will demonstrate the supremacy to other “bio”-packages and programming languages and convince you of, both the simplicity of our new API and the gains in performance. As a showcase, we will implement a read mapper using SeqAn3 and show how application development can be simplified with our software including vectorised and paralleised algorithms.
This tutorial is mostly suited for computational biologist and bioinformaticians with research focus on sequence analysis (e.g., genomics, metagenomics, assembly, read alignment, variant detection, etc.) Attendees should have an intermediate knowledge in programming. Some basic C++- knowledge is strongly recommended.
• What SeqAn 3 is and is capable of
• How to write tools with SeqAn 3
• Modern C++ features like Concepts, Ranges, and many more
Attendees must bring their own laptop.
• MacOS (g++-7 or higher) or Linux or BSD (g++-7 or higher)
• Cmake-3.0 or higher
• [optional] VirtualBox (We will provide a fully integrated Ubuntu VM with all necessary software pre-installed)
09:00 – 09:30: [talk] introduction to SeqAn3
09:30 – 09:45: [talk] present the hands on workshop
09:45 – 10:30: [hands-on] set-up and programming
10:30 – 11:00: coffee break
11:00 – 12:30: [hands-on] programming
12:30 – 13:30: lunch
13:30 – 15:00: [hands-on] programming
15:00 – 15:30: coffee break
15:30 – 16:30: [hands-on] programming and testing the application
16:30 – 17:00: [talk] the future of SeqAn3
• Modern C++, SeqAn3
• No special tools are required or used.
- Meetings and conferences