Citations
If you use Cuttlefish in your work, please include the citations appropriate to the version you ran.
Cuttlefish (original)
Section titled “Cuttlefish (original)”10.1093/bioinformatics/btab309
Jamshed Khan, Rob Patro. Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections. Bioinformatics, Volume 37, Issue Supplement_1, July 2021, Pages i177–i186.
Cuttlefish 2
Section titled “Cuttlefish 2”Khan, J., Kokot, M., Deorowicz, S. et al. Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2. Genome Biology 23, 190 (2022).
Cuttlefish 3
Section titled “Cuttlefish 3”Cuttlefish 3 appears as a proceedings paper at RECOMB 2026 (Research in Computational Molecular Biology). A preprint is on bioRxiv: 10.1101/2025.02.02.636161 (v2)
Jamshed Khan, Laxman Dhulipala, Prashant Pandey, and Rob Patro. Fast and Scalable Parallel External-Memory Construction of Colored Compacted de Bruijn Graphs with Cuttlefish 3. Proceedings of RECOMB 2026; preprint: bioRxiv (2025), v2.
Acknowledgement
Section titled “Acknowledgement”This work is supported by NIH R01 HG009937, and by NSF CCF-1750472 and CNS-1763680.