NGS Pre-Processing, Mapping and De Novo Assembly

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

Import a Wide Range of Formats

Raw data straight off the machine? Assembled results from a sequencing vendor? Analysis output from bioinformatics pipelines? Geneious 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

Clean 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

Don’t compromise on quality! 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 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


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

Tutorial- 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.

Tutorial- Assembling Chromatograms

Learn how to assemble and edit chromatograms for downstream analyses.

Tutorial- 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.

Application Notes

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 to reconstruct a complete, circular, annotated chloroplast genome from a short-read NGS data set.

Identification of Zika Virus

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