cuttlefishCuttlefish 2 efficiently constructs compacted de Bruijn graphs from sequencing reads or reference sequences. It provides parallel processing and memory optimization, making it suitable for large-scale genome assembly and analysis.Versions

v2.2.0 (default)

Tags: genome assemblyParameters

INPUT_FASTQ (file, multiple) required: Input FASTQ files containing sequencing reads.

kmer (int) required: K-mer length for graph construction.

cutoff (int) required: Frequency cutoff for (k + 1)-mers.

Links

License: BSD-3

Cite as: Khan, J., Kokot, M., Deorowicz, S. et al. Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2. Genome Biol 23, 190 (2022). https://doi.org/10.1186/s13059-022-02743-6

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