René Rahn, Temesgen Dadi (CIBI)
Athen, ECCB 2018 Tutorial
This tutorial will first introduce the C++ software library SeqAn for sequence analysis, including an overview of the contained algorithms and data structures (alignments, indices, IO, etc.) and applications (read pre-processing, read mapping, alignment tools replacing BLAST, variant detection, etc.) implemented with SeqAn and how they perform compared to other libraries and applications. In this introductory part the participants will setup their environment to start developing with SeqAn. The participants will then implement an application using many modules of the SeqAn library in a guided hands-on session. In the afternoon, there will be a general introduction into the workflow system KNIME and its capabilities. This part demonstrates a sample Workflow using tools from SeqAn and explains the basic principles of working with KNIME. This part is followed by another guided hands-on session, where the participants will learn how to create a tool description of their previously developed SeqAn application and how to integrate the respective tool into KNIME. This part is finalized by creating and executing a small sample workflow with the new tool including some simple exploration of the results.
In the end of this workshop an outline of the next generation of the SeqAn library, regarding its parallelization efforts, as well as the cloud execution of KNIME workflows will be given.
- What SeqAn is and is capable of
- How to write tools with SeqAn
- What KNIME is and is capable of
- How to incorporate and share existing tools within KNIME
- Practical experience with KNIME through an exercise on sequence analysis
This is a beginner tutorial for developers and users of applications in the domain of sequence analysis (read mapping, variant detection, metagenomics, RNseq, assembly, etc.), so no prior knowledge of SeqAn or KNIME is required, albeit it can be very helpful.
For the programming part a basic knowledge in C++ is required. Also, the following compilers are supported:
- GCC >= 4.9
- Clang/LLVM >= 3.5
- ICC >= 18.0
- Visual C++ >= 14 (Visual Studio 2015)
We will provide an ubuntu virtual machine with preinstalled software ready to use (requires virtual box installation and at least 40 GB of free disk space.)
The registration is already closed.
SeqAn, KNIME, Sequence Analysis
KNIME 3.6, SeqAn 2.4,