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 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 and Ion Torrent.

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.

How to Map NGS Reads to a Reference in Geneious Prime

How to Perform De Novo Assembly of NGS Reads in 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.

Mapping and SNP Calling – Learn how to perform a reference assembly with NGS data and to call SNPs on the assembled contig.

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.

More Geneious Prime Features

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

AlignmentPerform 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.
Charles MooreNovartis Pharma AG, Switzerland