SeqAn

SeqAn provides a C++ library of efficient algorithms and data structures for sequence analysis, enabling genome sequencing and next-generation sequencing (NGS) data processing and algorithm development.

Key Features:

• Efficient algorithms and data structures: Implements state-of-the-art components including assembly algorithms and BWT-based (Burrows–Wheeler Transform) read mappers for genome sequencing and NGS analysis.
• Generic design: Employs a generic C++ design philosophy to achieve high performance, extensibility, and seamless integration with other libraries while preserving algorithmic efficiency.
• Hardware acceleration support: Actively supports various hardware acceleration techniques to improve performance on large-scale biological data analyses.
• Algorithm benchmarking platform: Provides components used for experimenting with and comparing exact string matching algorithms and has been applied in a rewritten version of the MUMmer tool.

Scientific Applications:

• Genome sequencing and assembly: Supplies algorithms and data structures applicable to genome assembly workflows and related analyses.
• Read mapping and NGS analysis: Enables implementation of BWT-based read mappers and other methods for processing next-generation sequencing data.
• Algorithm development and benchmarking: Serves as a platform for developing, testing, and comparing sequence analysis algorithms.

Methodology:

Provides implementations of efficient data types and algorithms and supports hardware acceleration techniques for practical application in bioinformatics.