Map to Reference

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

Course Content

Map NGS Reads to a Reference

Select a reference sequence, choose a mapping algorithm, set the sensitivity and map to reference.
3 minutes

Explore Contig Documents

View the consensus sequence and quickly identify high or low coverage regions using the coverage graph.
3 minutes

Recommended Resources

Plugin - BBDuk Trimmer

Download the plugin for quality trimming and filtering your sequences.

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

Advantages and disadvantages of different map to reference algorithms.

Manual for Map to Reference

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

What function should I use?

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

More Geneious Academy

With this practical exercise, perform a reference assembly with NGS data and call SNPs on the assembled contig.
Watch the series and learn how to perform a de novo assembly of short-read NGS data and assemble circular contigs.
Watch how to perform multiple alignments and assess levels of homology among sequences before constructing a phylogeny.
Learn to align your chromatograms to a reference sequence, find variants and verify sequences in this video series.
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