NGS Visualization and Downstream Analysis

Beautiful visualization of annotated genomes and assemblies, powerful variant calling and RNA-Seq expression analysis.

Effortless NGS Visualization and Navigation

With just a click, get the visualization you need for the next generation sequencing data you have. Annotated genomes, circular genomes, mapped reads, contigs are all displayed in our highly customizable sequence view. Choose coloring schemes, graphs and tracks of additional annotations to display, then use dynamic annotation searching and location jumping to find what you’re looking for.

Powerful SNP Variants Analysis

Find SNP/Variants with either the versatile Geneious algorithm or well known FreeBayes. If you have variant calls from an external pipeline or provider, simply drag in a VCF. Identify novel variants by programmatic comparison with known variants or sort and filter using our dynamic tabular view then see the genomic context by switching to the synchronized sequence view.

RNA-Seq - Volcano Plot

Simple RNA-Seq Expression Analysis

Calculate expression levels from mapped reads then perform pairwise comparison between samples to identify differentially expressed genes. Without any expertise in the statistical programming language, R, use the industry standard DESeq2 package to compare expression between two conditions, each with replicate samples.

Switch to the PCA Plot tab to check the quality of your data using principal component analysis then switch to the interactive volcano plot to spot genes of interest. After selecting a gene in the volcano plot you can jump straight to it in the sequence view where all genes have heatmap coloring based on differential expression.

Amplicon Metagenomics

Assemble filter and analyze metagenomic datasets in Geneious Prime. Amplicon data can be classified using the Sequence Classifier or the 16S Biodiversity Tool.

Classify Amplicon Data with the Sequence Classifier


Expression Analysis – Learn to calculate normalized expression measures from RNA-Seq data. Measure RPKM, FPKM and TPM on datasets from two different sample conditions then calculate differential expression between the two samples.

Expression Analysis with DESeq2 – Learn how to use DESeq2 to compare expression levels for two sample conditions with replicates.

Amplicon Metagenomics – Learn how to assemble, filter and analyze a NGS metagenomic data set in Geneious Prime.

More Geneious Prime Features

Assembly and MappingDe novo assembly or reference mapping using industry leading algorithms, including TopHat and Velvet.

AlignmentPerform pairwise and multiple alignments of DNA or protein using trusted algorithms, including MAFFT and ClustalW.

Analysis and Annotation – Trim, assemble, annotate and view Sanger sequencing trace files

Molecular Cloning – View plasmid maps, automatically annotate vectors, find restriction sites; digest, ligate, and perform Golden Gate, Gibson, and Gateway cloning.

BLAST / NCBI – Connect to NCBI and PubMed, submit sequences directly to GenBank, BLAST sequences and search your own database.

Import Data – Import and convert common file types as well as their annotations and notes with a simple drag and drop

Geneious is an absolutely beautiful package to work with. We love it and we are telling everyone about it.
Charles MooreNovartis Pharma AG, Switzerland