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align.minimap2 ​

Liatir.align.minimap2() maps long or short reads to a reference with minimap2, using a preset for the read type.

Signature ​

ts
minimap2(args: Minimap2Args): Promise<AlignResult>

Arguments ​

ts
type Minimap2Args = {
  reference: string;   // reference FASTA
  reads: string;       // reads (FASTQ / FASTQ.gz)
  outputSam: string;   // where to write the output SAM
  preset?: string;     // 'sr' (short read), 'lr', 'map-ont', … (default 'sr')
  threads?: number;    // omit or use 0 to let Liatir choose a safe local value
};

Result ​

Returns the same AlignResult as bwaMem — ok, exitCode, stderr, outputSam, and the threads used.

Example ​

ts
const result = await Liatir.align.minimap2({
  reference: "/path/to/genome.fa",
  reads: "/path/to/reads.fastq.gz",
  outputSam: "/path/to/aligned.sam",
  preset: "map-ont",
});

Requires the minimap2 binary — check availability with Liatir.deps.check.