Map to Reference in Geneious Prime

Course Content

Map NGS Reads to a Reference

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

Explore Contig Documents

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

Assemble Coronavirus Genomes

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

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

TUTORIALHow to Map NGS Reads to a Reference and Call Variants
Map paired reads to the E. coli yghJ CDS, review coverage, then call and filter SNPs on the assembly.
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VIDEO SERIESDe Novo Assembly in Geneious Prime
Learn to assemble NGS reads without a reference genome, covering sensitivity settings, read normalization, and circular genome assembly in Geneious Prime.
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VIDEO SERIESMultiple Alignments in Geneious Prime
Choose the right alignment algorithm for your dataset size, from Muscle to MAFFT, then align multiple sequences and assess homology in Geneious Prime.
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VIDEO SERIESSanger Sequence Analysis in Geneious Prime
Trim and map Sanger chromatograms to a reference, then call SNPs, review their effect on protein coding, and export your variants.
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