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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 12-Core AMD Opteron
  • Memory:
    Internal: 128 GB ECC RAM
    Hard Disk space: 8 x 2TB HD (10 TB 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 2012 version

Data Import and Validation

  • input file validation jobs are run in the background now
  • new input features:
    • active directory compatible: only user-specific files and folders are displayed in the file-chooser
    • compressed .gz-files are accepted as input
    • paired end data in two separate files are paired automatically now and handled as one dataset in the GUI (displayed with two file sheets as icon); previous shuffling is not required anymore
  • paired end data statistics are given per input file (one for shuffled files, two for separate files)
  • pdf export: included read length distribution chartmapping is based on GMS_map version 3.5

Genomatix Mapper

  • new options:
    • linker removal: a file containing linker sequences can be submitted
    • separate 5'/3'-Masking of paired end data
    • mapping of data from directed antisense sequencing
  • output:
    • default alignment output is BAM (Gx alignment optionally) (can be converted to SAM on export)
    • default position output is BigBed (can be converted to BED on export)
    • mapping quality scores have been added

Structural Variant Detection

  • detection of duplications and intra-chromosomal translocations
  • input:
    • data mapped against a user library is accepted as input
    • command line version: generic paired end BAM files accepted as input
  • settings:
    • the following parameters can optionally be detected automatically: 'mean insert size', 'max deviation from mean', 'sigma threshold', 'strand orientation'
    • new parameter 'minimum mapping quality' replaces 'minimum quality distance'
  • output: VCF as new format
  • pdf export: included circos overview chart

Gene Fusion Detection

  • settings:
    • the following parameters can optionally be detected automatically: 'mean insert size', 'max deviation from mean', 'sigma threshold'
    • new parameter 'minimum mapping quality' replaces 'minimum quality distance'

SNP Detection

  • output: VCF as new format
  • Nucleotide quality scores are read as Phred scores and no longer as integer value of the ascii character given in the sequence read file (e.g. FASTQ)
  • settings: default value for parameter 'Min. Nucleotide Quality (Phred Score)' has been changed from 10 to 30

Small InDel Detection

  • output: VCF as new format
  • settings: parameter for 'maximum coverage' can be set to 'ignore'
  • pdf export: included insertion size and coverage size distribution charts

Velvet Assembly

  • input:
    • accepts paired end data from two separate files
    • compressed .gz-files are accepted
  • settings: parameter for strand orientation

GUI Performance

  • performance improvement for displaying projects
  • reduction of network traffic

Export

  • additional local download option in export view for files (up to 20 MB per default, limit can be configured)

Command Line Features

  • automatic detection of input file types
  • input files can be located in subdirectories of the input directory

Active Directory (AD)/LDAP support

  • system supports integration into existing AD/LDAP environment
  • account data is the same for GUI/command line ('gx_sesame.passwd' file is no longer needed)