HyperGen is a Rust library used to sketch genomic files and realize fast Average Nucleotide Identity (ANI) approximation. HyperGen leverages two advanced algorithms: 1. FracMinHash and 2. hyperdimensional computing (HDC) with random indexing as shown in the following figure:

HyperGen first samples the kmer set using FracMinHash. 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. The sketch size generated by HyperGen is 1.8 to 2.7× smaller than Mash and Dashing 2. ANI estimation in HyperGen can be realized using highly vectorized vector multiplication. HyperGen's database search speed for large-scale datasets is up to 4.3x faster than Dashing 2.

HyperGen requires Rust language and Cargo to be installed. We recommend installing HyperGen using the following command:

git clone https://github.com/wh-xu/Hyper-Gen.git
cd Hyper-Gen

cargo install --path .

Current version supports following functions:

Example:
hyper-gen-rust sketch -p ./data -o ./fna.sketch

Positional arguments:
-p, --path <PATH>               Input folder path to sketch
-o, --out <OUT>                 Output path 
-t, --thread <THREAD>           Threads used for computation [default: 16]
-C, --canonical <CANONICAL>     If use canonical kmer [default: true]
-k, --ksize <KSIZE>             k-mer size for sketching [default: 21]
-S, --seed <SEED>               Hash seed [default: 123]
-s, --scaled <SCALED>           Scaled factor for FracMinHash [default: 1500]
-d, --hv_d <HD_D>               Dimension for hypervector [default: 4096]
-D, --device <DEVICE>           Device to run [default: cpu] [possible values: cpu, gpu]

Example:
hyper-gen-rust 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]

• (a) Mash uses MinHash to sample kmer hash set and stores discrete hash values as the genome sketch.
• (b) HyperGen uses FracMinHash to sample kmer hash set and encodes discrete hash values into continuous sketch hypervector.

1. Weihong Xu, Po-kai Hsu, Niema Moshiri, Shimeng Yu, and Tajana Rosing. "HyperGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors." Under review.

For more information, post an issue or send an email to [email protected].