Whole genome alignment

What is whole genome alignment?

Whole genome alignment is the process of arranging large genome assemblies or contig sets against one another to identify corresponding blocks and their coordinates. It can reveal collinearity, rearrangements, substitutions, insertions, and deletions. MUMmer4 NUCmer uses exact matches as anchors and extends them into alignments, producing assembly-to-assembly evidence rather than a substitute for raw-read mapping or independently validated variant calls.

Use whole-genome alignment for comparing strains, assembly versions, haplotypes, related species, or a draft assembly against a reference. Reference choice, assembly quality, repeat content, ploidy, and evolutionary distance determine how coordinates and apparent rearrangements should be interpreted.

Review dot plots and coordinate tables before focusing on variants. Duplications, inversions, translocations, unplaced contigs, and repeat-driven multi-mapping can create several valid correspondences. Preserve delta files, filters, reference names, and coordinate conventions so every reported difference can be traced back to the alignment.

When to use whole genome alignment

• Best fit. Assembly comparison, synteny, rearrangements, polishing, and candidate differences
• Required input. Reference and query genome or contig FASTA files with assembly metadata

Benefits of whole genome alignment

• Clear correspondence. Scales to genome assemblies
• Connected evidence. Reports coordinate-aware differences
• Reusable output. Visualizes synteny and rearrangements

Primary limitations

• Method dependence. Assembly errors mimic variation
• Input dependence. Repeats create ambiguous matches
• Interpretive limit. Raw-read support is not included

Whole genome alignment methods

NUCmer identifies maximal exact matches between nucleotide sequences and clusters consistent anchors before extension. Match-mode and filtering settings change sensitivity and the number of repeated correspondences retained.

Dot plots summarize large-scale geometry, while coordinate and delta files preserve detailed alignments. SNP and indel reports should be interpreted only after repetitive and multiply aligned regions are understood.

Whole genome alignment applications

Whole genome alignment is best suited to assembly comparison, synteny, rearrangements, polishing, and candidate differences. The result can support comparative review, sequence curation, annotation, profile construction, phylogenetic preparation, structural interpretation, or experimental planning when those downstream uses match the alignment scope.

Keep the alignment as evidence rather than a conclusion. Downstream claims should remain tied to sequence provenance, coverage, method agreement, relevant biological context, and any independent structural, evolutionary, or experimental support.

How to run whole genome alignment online

Use the connected workflow to keep input records, method settings, native outputs, warnings, and exports together. Review every stage before using the result for annotation, phylogeny, variant interpretation, or experimental decisions.

1. Select assemblies. Choose a biologically appropriate reference and document assembly versions.
2. Check quality. Review contiguity, contamination, haplotype status, and repeat content.
3. Run NUCmer. Run MUMmer4 with explicit match mode, strand, and filtering settings.
4. Review genome geometry. Inspect dot plots, coverage, coordinates, duplications, and rearrangements.
5. Validate differences. Validate candidate variants or breakpoints with reads and orthogonal evidence.

How to interpret whole genome alignment results

A clean diagonal suggests broadly collinear assemblies; reverse diagonals indicate inversions, and off-diagonal blocks may represent translocations, duplications, or assembly placement differences.

Confirm major events using assembly graphs, raw-read mappings, or an independent method. Coordinate conventions and reference direction must remain explicit in every exported table.

How whole genome alignment works

MUMmer4 NUCmer aligns reference and query assemblies and returns coordinates, delta files, variants, statistics, and dot plots.

1. Select assemblies. Choose a biologically appropriate reference and document assembly versions.
2. Check quality. Review contiguity, contamination, haplotype status, and repeat content.
3. Run NUCmer. Run MUMmer4 with explicit match mode, strand, and filtering settings.
4. Review genome geometry. Inspect dot plots, coverage, coordinates, duplications, and rearrangements.
5. Validate differences. Validate candidate variants or breakpoints with reads and orthogonal evidence.

Inputs and outputs

Check formats before running, then inspect and download the result from every workflow step.

Inputs

• Alignment input. FASTA PDB mmCIF Reference and query genome or contig assemblies in FASTA format.

Outputs

• Alignment outputs. FASTA CSV TSV PDB JSON Delta and coordinate files, SNP and indel tables, alignment statistics, and dot plots.