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ReasmConfig

argenus::reassemble

Struct ReasmConfig 

Source 
pub struct ReasmConfig {
    pub minimap2: String,
    pub spades_py: PathBuf,
    pub spades_python: PathBuf,
    pub threads: usize,
    pub core_cov: f64,
    pub jobs: usize,
}
Expand description

Tool paths + tuning for the reassembly step.

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§minimap2: String§spades_py: PathBuf

Path to spades.py.

§spades_python: PathBuf

Python interpreter that can run SPAdes (its pixi env python; the system python is often too old). Empty => call spades_py directly on PATH.

§threads: usize§core_cov: f64

Fraction of a read covered by the ARG alignment to call it “core” (0.70).

§jobs: usize

Concurrent SPAdes jobs.

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