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. Liatir currently exposes a practical default configuration, with more preset controls planned.