NGS Pre-Processing, Mapping and De Novo Assembly

Import any data type, demultiplex, trim, filter, assemble or map to reference.

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
  • De-duplicate
  • 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.




NGS Visualization and Analysis

Comprehensive analysis of data, including genome browser, contig visualization, SNP calling, and RNA-Seq expression analysis.

Sanger Sequencing

Trim, assemble, and view Sanger sequencing trace files. Powerful SNP detection and variant calling.

DNA Sequence Alignment

Sequence alignment, visualization and editing. Select from multiple algorithms including Clustal Omega, MUSCLE and MAFFT.

Import Data

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


How to map to reference
How to perform de novo assembly
Mapping and SNP Calling tutorial
How to perform metagenomics analysis
Geneious is an absolutely beautiful package to work with. We love it and we are telling everyone about it.
Charles MooreNovartis Pharma AG, Switzerland