Mehr als nur Mapping.
Solutions

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 from Illumina (Genome Analyzer and HiSeq), SOLID, Helicos and 454 Life Sciences Sequencers for both single and paired 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 1U 19'' server enclosure with the hard disks built in.
  • Dimensions: 432 x 43 x 650 mm (17 x 1.7 x 25.6 inches) (W x H x D)
  • Weight: 19.5 kg (43 lbs)
  • Processor:2 x 6-Core AMD Opteron 2000
  • Memory:
    Internal: 64 GB ECC RAM
    Hard Disk space: 4 x 2TB HD (2TB for user data, 6 TB containing Genomatix' proprietary annotation data which will be replaced on updates)
  • Power Supply: 100-240 V, redundant 650 W AC power supplies w/ PFC, 60-50 Hz, 8-4 amps

Release notes

Release notes of the October 2011 version

New features

  • mapping is based on GMS_map version 3.5
    • CNVs normalized by mappability (requires sequence reads of equal length and mapping to a pre- installed genome)
    • BAM output includes probability values
    • Recognition of the new FASTQ format (see CASAVA V1.8 Changes)
  • GMS_snp
    • New parameters to control snp call (e.g. minimum nucleotide call quality, minimum overall alignment quality of sequence read, collapse of pileups etc.)
    • Enhanced summary report (e.g. transition vs transversion ratio and nucleotide coverage statistics)
  • small InDel module
    • detection of small InDels (up to ~10 bp, depending on read length)
    • statistics (number of detected insertions and deletions)
  • TViewer data generation module takes into account mappings to the splice junction library
  • Positional and alignment data are calculated in BigBed/BAM format internally but can be converted to BED/SAM on export

New features of the graphical user interface

  • Gene Fusion module
    • detection of gene fusions and read-throughs (across and within chromosomes) from paired-end RNA- Seq data
    • statistics (number of detected gene fusions, cluster size distribution)
  • structural variants module
    • detection of structural variants (large insertions, deletions, inversions and inter-chromosomal translocations) from paired-end DNA-Seq data
    • statistics (number of detected structural variants, cluster size distribution, variant size distribution)
    • visualization of structural variants and CNVs with CIRCOS (for the whole genome and for each chromosome)
  • PDF output for each analysis page for retrieval of graphics from the GUI in a printable document
  • public data export (allows everybody to see exported data)

Data changes

  • Small RNA library
    • improved library: over 400,000 sequences of experimentally verified non coding RNAs from 10 classes
    • sequences and annotation accessible
  • Updated genomes
    • Arabidopsis thaliana (TAIR10)
    • Bos taurus (NCBI build 5)
    • Danio rerio (NCBI build 4)
    • Sus scrofa (NCBI build 2)
  • New genomes
    • Oryctolagus cuniculus (rabbit, NCBI build 1)
    • Xenopus tropicalis (western clawed frog, NCBI build 1)
  • ElDorado versions 07-2008 and 12-2008 have been removed due to space constraints

Improved features

  • adaption of the "ambiguous" threshold leads to an increase in mapped reads
  • various small bug-fixes and improvements in ExonMapper