Sequence Aligner
Align sequences with minimap2
About the Sequence Aligner
This page runs minimap2 2.17 compiled to WebAssembly, so you can map reads to a reference or align assemblies entirely in the browser. Upload a reference and a query, pick the preset that matches your platform, and minimap2 handles the rest.
minimap2 is the default aligner across most of modern genomics. It is fast enough for whole genomes, accurate enough to replace older mappers for most tasks, and it uses a single -x preset to adapt its scoring to short reads, long reads, assemblies or spliced RNA.
Alignment is usually the step before everything that matters downstream: variant calling, expression quantification, peak calling and copy-number analysis all consume its output. Running it here means the reference and the reads never have to be uploaded anywhere.
What this tool does
Short-read mapping
The sr preset maps Illumina-style reads with end-to-end scoring, the standard choice for whole-genome and exome sequencing.
Nanopore mapping
The map-ont preset is tuned for the higher error rates and long read lengths of Oxford Nanopore data, including the k-mer weighting that handles its error profile.
PacBio HiFi mapping
The map-pb preset exploits the high accuracy of PacBio HiFi reads, using k-mer weighting to distinguish true matches from coincidental sequence similarity.
Assembly alignment
The asm presets align one assembly to another, used for scaffolding, reference replacement and genome comparison.
Spliced RNA alignment
The splice preset places reads across exon junctions, which is what makes transcript-aware quantification and junction calling possible.
Example commands
minimap2 --versionConfirm the aligner is loaded and report the build before starting a run.
minimap2 -ax sr ref.fa query.fqMap short Illumina reads to a reference with the sr preset.
minimap2 -ax map-ont ref.fa query.fqMap Oxford Nanopore reads, whose error profile needs k-mer weighting.
minimap2 -ax map-pb ref.fa query.fqMap PacBio HiFi reads, which are accurate enough for strict end-to-end scoring.
minimap2 -ax asm5 ref.fa query.faAlign an assembly to a reference, for scaffolding or reference replacement.
minimap2 -ax splice ref.fa query.fqAlign RNA-seq reads across splice junctions for transcript-aware analysis.
Frequently asked questions
Are my reference genome and reads uploaded?
No. minimap2 runs as WebAssembly in your browser. Both the reference and the query stay on your device, which matters for human and clinical data.
Which preset should I use?
Use sr for Illumina or other short high-accuracy reads, map-ont for Nanopore, map-pb for PacBio HiFi, asm5 for assembly-to-reference and splice for RNA-seq. If unsure, the platform preset is almost always right.
Why is my alignment rate low?
Common causes are the wrong reference assembly, a sample that is not what the metadata claims, adapter or contamination carryover from skipping QC, or an inappropriate preset. Run fastp quality control first and confirm the reference build matches.
What is the difference between asm5 and asm20?
asm20 is a higher-sensitivity preset for divergent or repetitive assemblies and is roughly three times slower. Use asm5 for same-species comparisons and asm20 when divergence is high or you expect gaps in the draft.
Does this produce a BAM file?
minimap2 writes SAM by default. The SAM/BAM Viewer on this site is the natural next step for inspecting the alignment header and flagstat output.
How large a reference can I load?
A human reference is a few gigabytes uncompressed and will strain most browsers, so a chromosome or a targeted region is a more realistic input here. For whole-genome alignment, run minimap2 locally.
Related tools
All processing happens locally in your browser. Nothing you upload is transmitted or stored, as described in the privacy policy.