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Minimap2 is a command-line aligner for mapping DNA or mRNA sequences to reference sequences. It supports several distinct jobs—including long-read genomic mapping, RNA alignment across splice junctions, short-read mapping, read-overlap finding, and assembly comparison—but the right command depends on the data and task. Its -x preset selects a workflow-specific configuration; first check that your installed version supports the preset you need.
What minimap2 does
Minimap2 aligns nucleotide sequences: it can map sequencing reads to a reference, find overlaps between long reads, or align assemblies against one another. The official project README lists use cases including PacBio and Oxford Nanopore genomic reads, PacBio Iso-Seq and Nanopore cDNA or Direct RNA reads, Illumina single- or paired-end reads, and whole-genome comparisons of closely related species.
The peer-reviewed 2018 methods paper describes applicability to accurate short reads of at least 100 bp, genomic reads of at least 1 kb with error rates around 15%, full-length noisy Direct RNA or cDNA reads, and assembly contigs or related chromosomes up to hundreds of megabases. These are ranges reported in the paper, not guarantees for every dataset or configuration. The method includes split-read alignment, concave gap costs for long insertions and deletions, and heuristics intended to reduce spurious alignments. Read the paper.
Choose a minimap2 preset by data and task
Use the -x option to choose a preset suited to your input and goal. The README documents map-ont as the default, but a default is not a universal best choice. Preset availability can depend on the installed version, so consult the README and manual for that version.
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| Input and task | Preset | Version note |
|---|---|---|
| Oxford Nanopore genomic reads | map-ont |
Documented current preset |
| PacBio CLR genomic reads | map-pb |
Documented current preset |
| PacBio HiFi/CCS genomic reads | map-hifi |
Documented for v2.19 and later |
| Nanopore Q20 genomic reads | lr:hq |
Documented for v2.27 and later |
| Short genomic paired-end reads | sr |
Documented current preset |
| Long spliced RNA reads | splice |
Consult the README for Direct RNA and high-quality Iso-Seq/Kinnex options |
| Short-read RNA-seq | splice:sr |
Documented for v2.29 and later |
| Intra-species assembly alignment | asm5 |
Documented current preset |
| Long-read overlap finding | ava-pb or ava-ont |
Choose based on PacBio or Nanopore input |
Preset settings are tuned for different data characteristics. For example, the README says map-pb uses homopolymer-compressed minimizers, while map-ont uses ordinary minimizers; the project reports that this choice benefits PacBio CLR sensitivity and performance but can hurt Nanopore reads. Avoid substituting presets solely because both inputs are long reads.
Install minimap2 from the official project
The project provides precompiled binaries through its linked releases and supports compiling from source. For a source build, the documented prerequisites are a C compiler, GNU make, and zlib development files. Start at the official repository and use its release links to find a build appropriate for your system; available versions and binaries can change.
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The repository warns that minimap2.com is a phishing site. Do not treat it as an official download source. The project also asks users to cite Heng Li’s 2018 paper, “Minimap2: pairwise alignment for nucleotide sequences.”
Build an index and align reads
A basic reference-mapping workflow has two commands. These examples follow the official README; they assume you have a reference FASTA file and reads in FASTQ format.
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Build an index from the reference:
minimap2 -d ref.mmi ref.fa -
Map reads and write SAM output:
minimap2 -a ref.mmi reads.fq > alignment.samRank #4
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Use the appropriate preset for your reads and task, for example by adding -x map-ont for Nanopore genomic reads. Minimap2 workflows can also emit PAF; choose the output format that fits the downstream tools you intend to use. The -a option in the example requests SAM output.
Understand what is fixed in an index
Indexing parameters including -k, -w, -H, and -I are set when the index is built and cannot be changed later during mapping. If different workflows require different index settings, build and retain separate indexes from the reference rather than expecting a mapping-time option to alter an existing .mmi file.
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What to expect from performance claims
The project README reports speed and accuracy comparisons against other tools, including comparisons involving roughly 10 kb noisy reads. Those are the project’s evaluations, not independent guarantees: performance depends on the workload, data, configuration, and system. The 2018 paper’s reported data ranges likewise describe the method’s demonstrated scope, not a promise of a particular result for a new sample.
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