Sanger Sequence Analysis in Geneious Prime

This Sanger sequence analysis series shows how to trim low-quality chromatogram ends and map them to a reference in Geneious Prime, then call SNPs on the resulting contig, review their predicted effect on protein translation, and export the variant data. The series spans two videos, 2 to 5 minutes each.

Course Content

Introduction to Sanger Sequencing

Trim poor-quality bases from chromatogram sequences, then map them to a reference with Align/Assemble > Map to Reference. Review the contig, edit bases, and save changes to the chromatograms or contig only.
LENGTH 5 minutes

Find Variants with Sanger Sequencing

Run Find Variations and SNPs on a Sanger contig, unselecting all four filter options to catch every disagreement. Review each SNP’s base change, frequency, and protein effect, such as a substitution or stop codon, then export results as CSV.
LENGTH 2 minutes

Recommended Resources

How do I assemble F and R pairs of sequences?

Use the Geneious de novo assembler to align pairs of Sanger sequences.

What Assembly Algorithm Ahould I Use?

Identify the most appropriate assembly algorithm for your data with this decision tree.

What Mapping Algorithm Should I Use?

This decision tree and validation table can help identify the most appropriate mapping algorithm for your data.

Manual for Creating, Viewing and Editing Sequences

Learn how to view, edit, translate, complement and translate sequences.

More Geneious Academy

TUTORIALHow to Assemble Chromatograms in Geneious Prime
Assemble bidirectional Sanger reads from blue tit mitochondrial DNA and extract high-quality consensus sequences.
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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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TUTORIALHow to Analyze Microsatellite Traces in Geneious Prime
Fit a ladder, call peaks, bin alleles and produce a genotype table with the Microsatellite plugin.
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VIDEO SERIESAnnotate Sequences in Geneious Prime
Annotate sequences in Geneious Prime by importing files, transferring or copying annotations between homologs, using a database, or annotating by BLAST.
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