Call and Compare SNPs

Perform a reference assembly with next-generation sequencing (NGS) data and call SNPs on the assembled contig.

Course Content

Calling SNPs

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

With this practical exercise, perform a reference assembly with NGS data and call SNPs on the assembled contig.
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In this in-depth video series learn how to assemble, filter and analyze an NGS amplicon metagenomic data set.
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