RESEARCH USE
Where minimap2 fits
minimap2 aligns long reads, short reads, spliced transcripts, or genome assemblies against a reference. Choose an official preset that matches the sequencing technology and task, then record the reference build, index, full command, output format, and version. Evaluate the output with alignment summaries and downstream quality checks appropriate to the experiment.
Research tasks
- Map long or short reads to a reference genome
- Run splice-aware alignment for RNA or cDNA reads
- Compare genome assemblies or identify long-read overlaps
What to evaluate before use
- Presets encode different error models and tasks; a parameter set should not be transferred across sequencing technologies without evaluation.
- Default PAF output may contain approximate coordinates without base-level alignment. The project also documents limitations in low-complexity regions and for small exons.
Verification note
This entry summarizes the tool's role without assessing scientific accuracy or endorsing its outputs. Features and terms can change; consult the official source before adopting it for consequential work.
sequence alignmentlong reads
Last verified: 2026-09-07
Source: official documentation ↗