Minimap2

Minimap2 is a versatile aligner for long reads, short reads, and assembled sequences. In Liatir it outputs SAM format.

Use it for

• long-read alignment;
• quick mapping experiments;
• alignment workflows where Minimap2 is the preferred mapper.

Inputs

• Reference FASTA or .mmi index.
• Reads FASTQ/FASTA.
• Threads.

Outputs

• SAM alignment file.
• Alignment log and parsed run summary where available.

How to read the result

The SAM output is usually an intermediate artifact. For downstream analysis, convert and sort it with Samtools or another alignment-processing tool.

Minimap2 supports many presets upstream. Liatir currently exposes a practical managed wrapper, and future UI work may expose more preset controls.

Technical details

Tool ID: minimap2

Liatir runs Minimap2 as a native tool, streams logs, and stores the generated SAM output in Results.