cuttlefish-rs-cli 0.0.1

Command-line interface to Cuttlefish 3: parallel, external-memory construction of uncolored and colored compacted de Bruijn graphs.
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# 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.

```bash
cargo install cuttlefish-rs-cli
```

This installs one binary, `cuttlefish`, with two subcommands:

```bash
# 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`][lib]. For full usage, resource controls,
output formats, and citation, see the [repository README][repo].

> 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.

[lib]: https://crates.io/crates/cuttlefish-rs
[repo]: https://github.com/COMBINE-lab/cuttlefish