BufBOSS

BufBOSS implements a buffering mechanism to enable efficient additions and deletions to dynamic de Bruijn graphs for genomic analyses such as genome assembly, variant detection, and compact storage of assembled genomes.

Key Features:

• Buffering mechanism: Temporarily stores data intended for addition or deletion to manage updates to the graph structure efficiently.
• Dynamic update support: Enables additions and deletions on compressed dynamic de Bruijn graphs.
• Elimination of dynamic bit vectors: Removes reliance on dynamic bit vectors, addressing their theoretical and practical slowness.
• Performance trade-offs: Offers trade-offs in time, memory, and disk usage relative to existing solutions.
• Improved deletion speed: Demonstrates superior deletion performance, reported as an order-of-magnitude improvement over prior methods.
• Comparative evaluation: Directly compared against Bifrost, DynamicBOSS, and FDBG in empirical assessments.

Scientific Applications:

• Genome assembly: Supports dynamic updates to de Bruijn graphs used in genome assembly workflows.
• Variant detection: Applicable to graph-based variant detection methods that require incremental updates.
• Storage of assembled genomes: Enables compact and updatable representations for assembled genomes.
• Dynamic graph manipulation: Facilitates scalable manipulation and maintenance of de Bruijn graphs in genomic studies.

Methodology:

Temporarily buffers additions and deletions to the compressed de Bruijn graph to avoid dynamic bit vectors and empirically evaluates time, memory, disk usage, and deletion speed against Bifrost, DynamicBOSS, and FDBG.