NGS Visualization and Downstream Analysis

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

Effortless Visualization and Navigation

With just a click, get the visualization you need for the data you have in front of you. 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.


Download a free trial and one of our tutorials to get to grips with the functionality of Geneious interactively.

Tutorial- 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.

Tutorial- Expression Analysis with DESeq2

Learn how to use DESeq2 in Geneious to compare expression levels for two sample conditions with replicates.

Application Notes

Identification of Zika Virus with Geneious

Explore a pipeline in Geneious which allows accurate identification and analysis of low concentrations of ZIKV from high-throughput metagenomic data proceeding from a patient with suspected infection.

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