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Map to Reference

Use the map to reference tool to map next-generation sequencing data against a reference, and assemble coronavirus genomes.

Map NGS Reads to a Reference

INSIDE THE VIDEO
Select a reference sequence, choose a mapping algorithm, set the sensitivity and map to reference.

  • Map to reference
  • View your results

LENGTH
3 minutes

Explore Contig Documents

INSIDE THE VIDEO
View the consensus sequence and quickly identify high or low coverage regions using the coverage graph.

  • Set your colours
  • Consensus quality
  • Coverage

LENGTH
3 minutes

Assemble Coronavirus Genomes

INSIDE THE VIDEO
A workflow for assembly of coronavirus genomes generated by tiled amplicon RT-PCR followed by Illumina sequencing.

  • Trim with BBDuk Plugin
  • Map to reference
  • Consensus sequence

LENGTH
4 minutes

Recommended Resources

MAP TO REFERENCE

TUTORIAL
Practice Mapping and SNP Calling

A practical exercise in reference assembly using next-gen sequencing data.

FAQ
Which map to reference assembly algorithm is best for my data?

Advantages and disadvantages of different map to reference algorithms.

MANUAL
Instructions for Map to Reference

A guide to using the map to reference tools in Geneious.

FAQ
What function should I use?

The difference between Pairwise/Multiple alignment, de novo Assembly, and Map to Reference.

GENEIOUS ACADEMY

How to perform metagenomics analysis
How to perform de novo assembly
How to perform multiple alignments
How to perform Sanger Sequencing