Mehr als nur Mapping.

Genomatix Mining Station (GMS)

The Genomatix Mining Station (GMS) offers high-performance alignment of Next Generation Sequencing (NGS) reads onto genomes, transcriptomes, small RNA and splice junction libraries. With its intuitive user interface, the GMS helps you quickly execute tasks such as genomic positioning, SNP and InDel detection, splice analyses, gene fusion and structural variant analysis and the identification of copy number variations. And the station stays flexible throughout your experiment.

The Genomatix Mining Station is a turn-key solution that gets you started within minutes of delivery and gets you highest quality results in very short time.

In combination with the Genomatix Genome Analyzer you get a fully integrated analysis solution from raw sequencing reads to the interpretation oft he biology behind your data. Being accessible via intranet from every desktop in your organisation will keep your internal workflows straight-forward and efficient.

Key features

Key features of the Genomatix Mining Station (GMS)

  • extremely fast and flexible mapping algorithm, allowing for multiple insertions or deletions
  • mapping to genomes and transcriptomes of 31 organisms. You can add your own sequences as a reference for mapping reads.
  • detection of known and de-novo splicing events
  • support for bisulfite sequencing reads
  • SNP analysis
  • Detection of gene fusions and structural variants
  • CNV analysis
  • statistics and classification of reads based on our excellent proprietary genome annotation
  • support for sequence- and color-based tags of any length (starting from 25 nucleotides) from all major sequencing equipment providers for both single and paired end reads
  • intuitive graphical user interface
  • All results can directly be handed down to the Genomatix Genome Analyzer. Adherence to standard output formats provides compatibility with your own pipelines.
  • Dedicated hardware server solution based on the reference-platform for AMD Opteron™ processors.

Technical data


Technical Data for the GMS:
  • Description: The Genomatix Mining Station consists of a 2U 19'' server enclosure with the hard disks built in.
  • Dimensions: 437 x 89 x 648 mm (17.2 x 3.5 x 25.5 inches) (W x H x D)
  • Weight: 29.9 kg (55 lbs)
  • Processor:2 x 16-Core AMD Opteron
  • Memory:
    Internal: 128 GB ECC RAM
    Hard Disk space: 8 x 2TB HD (10TB for user data, 6 TB containing Genomatix' proprietary annotation data which will be replaced on updates)
  • Power Supply: 100-240 V, redundant 720 1+1 W AC power supplies w/ PFC, 60-50 Hz, 9-4 amps

Release notes

Release notes of the April 2013 version

Small Variant Detection (version 1.1)

  • additional parameters:
    • Remove sequence duplicates
    • Extended BAQ computation (BAQ is the Phred-scaled probability of a read base being misaligned)


Release notes of the December 2012 version

Data content

  • new libraries for mapping based on the genomes of the latest ElDorado release (15 updated genome versions, including mouse, chicken, drosophila and c. elegans)

Genomatix Mapper

  • Sequences located on "unknown" chromosomes are now included in the mapping libraries and can be mapped against.
  • The mapper needs less memory reducing the time needed to load the library at the beginning of a mapping.

new task: Small Variant Detection

  • New 'Small Variant Detection' task based on the samtools package:
    • both SNP and InDel detection combined in one task
    • one VCF output for all small variants (e.g. for later use in the Variant Analysis task on the GGA)