cuttlefish-rs-cli

The Cuttlefish 3 command-line program: parallel, external-memory construction of uncolored and colored compacted de Bruijn graphs from reference sequences or sequencing reads.

cargo install cuttlefish-rs-cli

This installs one binary, cuttlefish, with two subcommands:

# construct a compacted graph
cuttlefish build --ref --seq refs.fa -k 31 --work-dir work --output graph

# decide whether two unitig FASTA files describe the same graph, up to
# strand and cyclic rotation
cuttlefish compare -a graph.fa -b other.fa -k 31 --work-dir cmp

The default build links jemalloc. --no-default-features selects the system allocator, and --features mimalloc selects mimalloc.

For the library, see cuttlefish-rs. For full usage, resource controls, output formats, and citation, see the repository README.

Cuttlefish 3 is under active development. The command-line interface and the private intermediate formats may still change before a stable release.

Distributed under the BSD 3-Clause License.