Science Score: 54.0%
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org -
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○Scientific vocabulary similarity
Low similarity (2.9%) to scientific vocabulary
Repository
Library for finding syncmers from &[u8] in rust
Basic Info
- Host: GitHub
- Owner: jguhlin
- License: mit
- Language: Rust
- Default Branch: main
- Size: 24.4 KB
Statistics
- Stars: 6
- Watchers: 2
- Forks: 2
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
Syncmers Library in Rust
Syncmers as defined by Dutta et al. 2022, https://www.biorxiv.org/content/10.1101/2022.01.10.475696v2.full Esp Fig 1b / Algorithm 1. Planning to implement other methods soon.
Definition
Using the parameterized syncmer scheme, a syncmer is a kmer whose smallest smer is at a given target position (t).
Extract Syncmers from &[u8]
rust
let sequence = b"CCAGTGTTTACGG";
let syncmers = find_syncmers(5, 2, &[2], None, sequence);
assert!(syncmers == vec![b"CCAGT", b"TTACG"]);
println!("{:?}", syncmers);
Extract Syncmers from &[u8], downsampling to 20%
rust
let sequence = b"CCAGTGTTTACGG";
let syncmers = find_syncmers(5, 2, &[2], Some(0.2), sequence);
assert!(syncmers == vec![b"CCAGT", b"TTACG"]);
println!("{:?}", syncmers);
Extract Syncmers from &[u8], keeping 80%
rust
let sequence = b"CCAGTGTTTACGG";
let syncmers = find_syncmers(5, 2, &[2], Some(0.8), sequence);
assert!(syncmers == vec![b"CCAGT", b"TTACG"]);
println!("{:?}", syncmers);
Find positions of Syncmers
rust
let sequence = b"CCAGTGTTTACGG";
let syncmer_positions = find_syncmers_pos(5, 2, &[2], None, sequence);
println!("{:?}", syncmer_positions);
assert!(syncmer_positions == vec![0, 7]);
TODO
Make sure X's are never the start / end of syncmers
Changelog
0.1.4: Added downsampling support
Owner
- Name: Joseph Guhlin
- Login: jguhlin
- Kind: user
- Location: Dunedin, New Zealand
- Website: http://www.josephguhlin.com/
- Repositories: 82
- Profile: https://github.com/jguhlin
Plant Genomicist and Bioinformatician interested in structural variation and pangenomics.
Citation (CITATION.md)
Please cite: https://www.biorxiv.org/content/10.1101/2022.01.10.475696v2 aka https://doi.org/10.1101/2022.01.10.475696
GitHub Events
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