Fast and Scalable Parallel External-Memory Construction of Colored Compacted de Bruijn Graphs with Cuttlefish 3.

ABSTRACT: The rapid growth of genomic data over the past decade has made scalable and efficient sequence analysis algorithms, particularly for constructing de Bruijn graphs and their colored and compacted variants critical components of many bioinformatics pipelines. Colored compacted de Bruijn graphs condense repetitive sequence information, significantly reducing the data burden on downstream analyses like assembly, indexing, and pan-genomics. However, direct construction of these graphs is necessary as constructing the original uncompacted graph is essentially infeasible at large scale. In this paper, we introduce Cuttlefish 3, a state-of-the-art parallel, external-memory algorithm for constructing (colored) compacted de Bruijn graphs. Cuttlefish 3 introduces novel algorithmic improvements that p

SUBMITTER: Khan J 

PROVIDER: S-EPMC11838517 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature