NGS analysis workflow

What packages are available?

map & more

The map & more package includes the mapping onto the genome, transcriptome and/or splice junction reference libraries of the selected organism. We can also map your data to a small RNA library and predict novel microRNAs.

Additionally you will receive quality metrics and statistics for the mapping.

We support basecode as well as colorcode reads from all major sequencing platforms. Paired-end data or bisulfite treated sequences can also be mapped.


This package adds gene fusion and structural rearrangement
analysis from the mapped data*,

You will also receive a one month online account on our server
enabling you to analyze your data for SNPs and view copy number
variations calculated from your data.


* paired-end data is required for these

biology complete

This package brings you the full interpretative power only Genomatix can provide by adding a one month Genomatix Genome Analyzer (GGA) account.

This includes all the software modules of the Genomatix Software Suite plus the extended functionality of the NGS analysis software.

Our software will enable you to:

  • call peaks/clusters from the mapping results
  • visualize and correlate your data within our comprehensive genome annotation including comparative genomics for 29 organisms
  • conduct scientific analyses in genomic context, to interpret associated gene regulation mechanisms or to look for expression patterns in your data
  • generate and evaluate networks and pathways related to or based on your data
  • create your own tf binding site definitions or use the full power of our matrix library to analyze promoters
  • perform extended literature searches to automatically extract knowledge from publications that is relevant for your project

All this and more can be done by simply logging into the account provided from any internet-connected computer using a standard browser software.
Your mapping results will come pre-loaded into the account, so can start to work on it immediately.


Here is an overview of the features coming with each package:

featuremap & morevariantsbiology complete
High quality alignment of NGS reads to genome, transcriptome, and/or small RNA library
Coverage of known and novel splice junctions
Read classification statistics
Comprehensive report and file descriptions
0.5 TB hard disk (with read & result files)
Detection of SNPs
Detection of structural variants
Detection of gene fusions
Detection of CNVs relative to reference genome
Intuitive web-based GUI (e.g. for SNP Analyses)
Support via email
Complete RNA-Seq workflow
Complete ChIP-Seq workflow
Retrieval and visualization of extensive genome annotation (31 species)
Comparative genomics
Correlation of genomic regions
Access to extensive TF binding site data base and analysis (MatInspector)
Gene regulatory module analysis
Literature information from expert curation and data mining
Pathway and gene enrichment analyses
Project and result management
Intuitive web-based GUI for data interpretation


For additional input on your analysis and results you can book the expert knowledge of our consulting team.

available species

The mygenomatix services are currently vailable for these organisms:


  • Homo sapiens (human)
  • Macaca mulatta (rhesus monkey)
  • Pan troglodytes (chimp)
  • Mus musculus (mouse)
  • Rattus norvegicus (rat)
  • Equus caballus (horse)
  • Canis lupus familiaris (dog)
  • Bos taurus (cow)
  • Sus scrofa (pig)
  • Monodelphis domestica (opossum)
  • Ornithorhynchus anatinus (platypus)
  • Danio rerio (zebrafish)
  • Gallus gallus (chicken)
  • Taeniopygia guttata (zebrafinch)


  • Arabidopsis thaliana (thale cress)
  • Vitis vinifera (wine grape)
  • Populus trichocarpa (western balsam poplar)
  • Oryza sativa (rice)
  • Sorghum bicolor (sorghum)
  • Glycine max (soybean)
  • Zea mays (corn)


  • Anopheles gambiae (mosquito)
  • Drosophila melanogaster (fruitfly)
  • Apis mellifera (honeybee)


  • Saccharomyces cerevisiae (baker's yeast)
  • Schizosaccharomyces pombe (fission yeast)
  • Neurospora crassa (neurospora)


  • Caenorhabditis elegans (nematode)
  • Plasmodium falciparum (plasmodium)

sample screenshots

Here are some sample screenshots of the data interpretation options:

quality control Get quality metrics on your sequencing experiment.
chip-seqThe ChIP_Seq workflow can help you define your own binding site motifs.
pathwaysGet the relevant pathways and networks for your genes.
GenomeInspector correlations Find correlations between your results and/or annotated features.
mappingStatistics for unique, multiple and ambiguous hits.
rna-seqAssess differential expression using the RNA workflow.
Transcriptome ViewerInspect alternative transcripts and their expression.
Literature analysis Easily scan the literature for information relevant to your details.