Call and Compare SNPs in Geneious Prime

Course Content

Calling SNPs

Comparing SNPs

Calling SNPs

How to use the Geneious variant finder to find SNPs in mapped data and set the parameters to filter out sequencing errors.

LENGTH 2 minutes

Comparing SNPs

How to filter SNPs based on their overlap with another annotation track or annotation type and filter out SNPs in regions of low coverage.

LENGTH 2 minutes

Recommended Resources

Can I call SNPs on individual sequences aligned to a reference?

How to call SNPs on different assmeblies and alignments.

Manual for Finding Variations/SNPs

A guide to using the Find Variations/SNPs feature in Geneious.

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.

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.

VIDEO SERIESExpression Analysis in Geneious Prime

Calculate and compare normalized expression measures from RNA-Seq data using the Geneious expression analysis tool.

VIDEO SERIESDe Novo Assembly in Geneious Prime

Assemble short-read NGS data from scratch in Geneious Prime, including read normalization and circular contig assembly.

VIDEO SERIESMetagenomic Analysis in Geneious Prime

Assemble, filter and analyze an NGS amplicon metagenomic dataset.

Get started with Geneious today

Try Geneious Free Pricing