Sdust.cr

Reimplementation of Sdust in Crystal.

• symmetric DUST algorithm

Installation

Install via GitHub Releases or from source:

git clone https://github.com/kojix2/sdust.cr
cd sdust.cr
shards build --release
# shards build --release -Dpreview_mt # enable multi-threading

Usage

Usage: sdust [options] <in.fa>
    -w, --window SIZE                Window size [64]
    -t, --threshold SIZE             Threshold size [20]
    -@, --threads INT                Number of threads [4]

License

• This project is a reimplementation of Heng Li's Sdust in Crystal.
• Sdust is part of Minimap2, which is licensed under the MIT License.

MIT License

FAQ

Q: Is this implementation faster than the original Sdust?

A: No, it's about 1.5 times slower. However, it becomes quite fast when multi-threading is enabled.

Q: Does this implementation consume less memory than the original Sdust?

A: No, it appears to consume about 5 times more memory. Enabling multi-threading further increases the consumption.

Q: Why was it created?

A: It was created to explore how much performance could be improved using Crystal, a language similar to Ruby.