dotANI first samples the kmer set and then estimate intersection via dotHash. Then the kmer hashes are encoded into hyperdimensional vectors (HVs) using HDC encoding to obtain better tradeoff of ANI estimation quality, sketch size, and computation speed. To obtains the cardinality of genomes, we use UltraLogLog (ULL). The sketch generated by dotANI has 2 parts, the dotHash sketch and ULL sketch. ANI estimation in dotANI can be realized using highly vectorized vector multiplication. dotANI also provides database search.
dotANI requires Rust language and Cargo to be installed.
We recommend installing HyperGen using the following command:
git clone https://github.com/jianshu93/dotANI.git
cd dotANI
# Without GPU acceleration for sketching
cargo build --releasedotANI supports GPU acceleration. Using GPU mode will require the installation of NVIDIA GPU driver. Use nvidia-smi or nvcc -V to check if the driver is installed. Then run the following command to install with GPU support:
# With GPU acceleration for sketching and distance calculation, tested on RTX 3090
cargo build --release --features cuda
Currently only Nvidia GPUs are supported. We tested the compatibility on both desktop RTX4090 and laptop RTX4060 with CUDA Version 12.x.
Current version supports following functions:
Example:
dotani sketch -p ./data -o ./fna.sketch
Usage: dotani sketch [OPTIONS] --path <path> --out <out>
Options:
-p, --path <path> Input folder path containing .fna/.fa/.fasta files (gzip/bzip2/xz/zstd compressed files supported, e.g., .fna.gz, .fa.bz2, .fasta.xz, .fna.zst)
-o, --out <out> Output DotHash sketch file
-T, --threads <threads> Number of threads, default all logical cores
-C, --canonical <canonical> Whether to use canonical k-mers [default: true] [possible values: true, false]
-k, --ksize <ksize> k-mer size for sketching [default: 16]
-S, --seed <seed> Hash seed [default: 1447]
--ull-p <ull_p> UltraLogLog precision parameter [default: 14]
-d, --hv-d <hv_d> Dimension for hypervector [default: 4096]
-Q, --quant-scale <quant_scale> Scaling factor for HV quantization [default: 1.0]
-h, --help Print help
-V, --version Print versionExample:
dotani dist -r fna1.sketch -q fna2.sketch -o output.ani
Positional arguments:
-r, --path_r <PATH_R> Path to ref sketch file
-q, --path_q <PATH_Q> Path to query sketch file
-o, --out <OUT> Output path
-t, --thread <THREAD> Threads used for computation [default: 16]
-a, --ani_th <ANI_TH> ANI threshold [default: 85.0]dotANI supports offloading the kmer hashing and sampling steps to GPU to speed up the sketching process. Use the following command to run on GPU device:
dotani-cuda sketch -p ./data -o ./fna.sketch
dotani-cuda dist -r fna1.sketch -q fna2.sketch -o output.ani