Import a Wide Range of Formats
Raw data straight off the machine? Assembled results from a sequencing vendor? Analysis output from bioinformatics pipelines? Geneious Prime has it all covered. Simply drag and drop to import FASTQ, FASTA, BAM, VCF, GFF and other formats from almost any sequencing machine including Illumina, PacBio, Nanopore, Ion Torrent and 454.
Extensive Pre-Processing of Sequencing Reads
Clean sequence data is critically important for accurate downstream analysis. Make sure your data is in tip-top shape by taking advantage of easy access to all of the necessary pre-processing tools:
- Demultiplex/split by barcode
- Trim and filter by read quality
- Trim adapters
- Merge paired reads
- Error correct and normalize
- Filter out chimeras
Reliable Reference Mapping
The exclusive Geneious Read mapper with its iterative approach produces superior results when compared to other popular mapping algorithms and can correctly align structural variants. If you need something a bit different, Bowtie, TopHat and BBMap are all at your fingertips.
Flexible De Novo Genome Assembly
The Geneious Assembler is ﬂexible enough to handle data from any type of sequencing machine with reads of any length, including paired-reads and mixtures of reads from different sequencing machines. It’s particularly good for microbial assemblies with the unique capability to produce circular contigs. Alternatively, running MIRA, SPAdes, Tadpole or Velvet is just as easy, and MAUVE genome alignment is on hand to help you with genome comparison and finishing.
Mapping, Coverage and Variant Calling using Geneious Prime
De Novo Assembly – Learn how to perform a de novo assembly of short read NGS data, how to work with paired-end data and check quality of an assembly against a reference sequence.
Assembling Chromatograms – Learn how to assemble and edit chromatograms for downstream analyses.
DNA Forensics – The aim of this module is to edit and analyse some “raw” DNA sequence data to determine the origin of a biological sample from a wildlife forensic case.
Circular De Novo Assembly – In this study two mitochondrial genomes are assembled from short-read NGS sequence data using the Geneious de novo assembler and the results compared with assemblies produced by Velvet, MIRA and SPAdes.
De Novo Assembly of a Bacterial Genome – A workflow for assembly and annotation of a bacterial genome from Illumina MiSeq data.
De Novo Assembly of Chloroplasts – Use Geneious Prime to reconstruct a complete, circular, annotated chloroplast genome from a short-read NGS data set.
Identification of Zika Virus – Explore a pipeline which allows accurate identification and analysis of low concentrations of ZIKV from high-throughput metagenomic data.
More Geneious Prime Features
NGS Visualization and Analysis – Comprehensive analysis of data, including genome browser, contig visualization, SNP calling, and RNA-Seq expression analysis.
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
I have found Geneious to be one of the most intuitive and powerful sequence analysis programs that I have used in all my years working in the molecular biology field. Thanks for making my life so much easier.
Geneious is an absolutely beautiful package to work with. We love it and we are telling everyone about it.
This program is wonderful! I was desperately looking for a software program that would make analyzing my sequencing data less painful. Thank you for developing a quality, user-friendly program. The interface is great!
Geneious is paramount in my research so I can’t be without it for too long.
The combination of powerful analytic features, intuitive navigation and file organization, and the responsiveness that representatives have shown to the inclusion of new functions has made us big fans of this software.
Geneious is a great software… I just want to express my appreciation to Biomatters to come up with such good product.
For many years I’ve wanted a friendly, menu-driven interface to our Glimmer program, but my research group has never had the resources available to build one. The Geneious Glimmer interface is terrific; it will allow any scientist to find genes in almost any bacterial, viral, or archaeal sequence, without requiring background expertise in Unix command-line programs. I’m also very pleased that Geneious makes Glimmer available across multiple computer platforms, including Windows and Mac.
We’ve been using our Geneious licenses a lot and really like the software. We’ve written several plug-ins ourselves and are using it more and more to analyze our data.
It’s not just about the buttons. From a user’s perspective, Phobos generates annotations, and Geneious handles annotations beautifully. The integration was obvious! And from a technical perspective it was easy to achieve, because it was simple to parse the outputs from Phobos into repeat annotations for the Geneious interface.
TopHat is a robust tool, but it was designed with experienced bioinformatics scientists in mind. Geneious makes TopHat accessible to many more users through the same powerful, intuitive user interface they have with other Geneious analysis tasks.