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.
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.
Mapping, Coverage and Variant Calling using Geneious Prime
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.
More Geneious Prime Features
Assembly and Mapping – De novo assembly or reference mapping using industry leading algorithms, including TopHat and Velvet.
Alignment – Perform 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.
We bought Geneious to work with Illumina datasets, and were delighted in its power and intuitive interface. It really takes advantage of multi-core processing, assembling tens of millions of reads to a reference sequence in minutes on a desktop system. And the strong user community means that help is not far off—hours after I posted a thread about a task I wanted to do, another user had a perfect solution! Finally we have an integrated system at an affordable price for all our DNA sequence analysis needs. Thanks, Geneious.
Geneious is the perfect combination of ease-of-use and bioinformatic refinement. Students easily grasp many of the concepts of bioinformatics because the sequence data is visualized so well. As researchers, we routinely use its functionality to perform data analysis on real data.