GeneXplainer Server and Workstation is a secondary and tertiary analysis tools for next-generation sequencing (NGS) data.

 

 

The server provides a wide range of analysis tools on a single IT platform with a user-friendly graphical interface.

  • a high performance computer designed to effectively tackle all genomics tasks
  • filled with professional software tools – mostly open source – for assembly and analysis
  • warranty and software support
  • all at an affordable price
  • processing next generation data from Illumina, Life Technologies and Roche platforms (extension types: .fastq, .csfasta/.qual and .fna/.qual)
The features of GeneXplainer Server were designed to create a complete tool, serving your data analysis needs from beginning to end.  

GeneXplainer Server’s wizard-like user interface is very easy to use and provides interactive help on each screen. The features of GeneXplainer Server were designed to create a complete tool, serving your data analysis needs from beginning to end. We have set default values that are safe, secure and convenient. You can use the product right out of the box without worrying without installations, drivers, parameters and options that make many bioinformatic tools difficult to use.

Applications

Genotyping

Reference assembly

De novo assembly

RNA-Seq

Copy Number Variation (CNV)

Multiple Sequence Alignment

 

Specification

Form factor/height: 2U Rack

Processor: Two 8-core Intel Xeon E5-4600 series processors (max. 4)

Memory: 96 GB LR-DIMM (max. 1.5 TB)

Hard Disk: 12TB HD  RAID support

Operating system: Ubuntu Linux 13.10

Warranty: 3-year customer replaceable unit and on-site limited warranty, next business day 9x5, service upgrades available


GeneXplainer Workstation is a fully-integrated system for gene expression analysis, variant calling, annotation, de-novo assembly, multi-sample comparison and all related data management and storage. It is designed for operational support of research and clinical laboratories using next generation sequencing technologies. GeneXplainer supports sequence data from both Illumina and Ion Torrent platforms. 

GeneXplainer Workstation is a combination of a powerful PC and a set of versatile, easy-to-use and customized software applications.   

 

Applications

Identifying novel isoforms and isoform switching events in RNA-Seq data;

Analysis of metagenome data to discover enzyme candidates;

Pathway association based on genetic variations and clinical data;

Disease association studies based on exome sequencing data

Primer design for multiplex PCR reactions

 

Specification

Form factor/height: Tower 17.5"

Processor: Intel Xeon E5-1620 3.60GHz

Memory: 32GB DDR3-1600 (max. 192GB)

Hard Disk: 3TB SATA

Operating system: Windows 8 Pro / Ubuntu Linux 13.10

Warranty: 3-year limited warranty, next business day 9x5, service upgrades available

All GeneXplainer's  flexible design structure enables us to seamlessly integrate any further applications into the same, familiar platform that you have already got used to. Our engineers can develop solutions for the special needs of your lab research, including custom database search and integration; annotation, motif search and novel element discovery; visualization; sequence analysis and manipulation tools; complex statistics (multisample comparison, normalization, clustering etc.); quality control and improvement tools.

 

Benchmarks

De novo assembly

Complete de novo assembly of a previously unknown bacteria in color space, including color code translation, generation of contig files etc.

 

Number of reads:

61 696 446

Total number of assembled contigs:

43 417

Read length:

35 bp (colors)

Total run time:

118 min 40 sec

 

ChIPSeq analysis pipeline

A complete analysis from raw data input to results, including mapping, peak detection, file generation etc. Default settings were used for the assembly and peak detection software tools.

 

Genome:

Mus musculus (m37)

Genome size:

2 716 965 481 bp

Number of reads:

5 474 809

Read length:

36 bp

Total time:

4 min 40 sec

Mapping time:

1 min 35 sec

Peak detection time:

1 min 28 sec

 

Reference assembly, gapped

Reference assembly in base space of a human genome from Illumina short reads. During the assembly not just the perfect matches were mapped but reads were aligned with both gaps and mismatches too.

 

Genome:

Homo Sapiens (GRCh37)

Genome size:

3 101 788 170 bp (according to estimations of the Genome Reference Consortium)

Number of reads:

83 000 000

Read length:

36 bp

Run time:

47 min 39 sec

 

Reference assembly, ungapped

Reference assembly in base space of a human genome from Illumina short reads. Ungapped alignment, no mismatches are allowed.

 

Genome:

Homo Sapiens (GRCh37)

Genome size:

3 101 788 170 bp (according to estimations of the Genome Reference Consortium)

Number of reads:

83 000 000

Read length:

36 bp

Run time with longer seeds:

36 min 59 sec

Run time with shorter seeds:

10 min 17 sec