• KeyGene and GENALICE extend their collaboration on big data for crop improvement

    Saturday 14 January 2017

    Harderwijk, Wageningen, the Netherlands – Today, at the first day of the international Plant and Animal Genome XXV Conference in San Diego, the Crop Innovation Company KeyGene and genomic big data solutions company GENALICE, announce the continuation of their strategic partnership. Jointly the companies will stand unmatched in exploiting the tremendous value of genomics related big data analysis in crop innovation.

    The KeyGene Vision – an expert’s perspective on agrigenomics & crop innovation

    KeyGene supports its customers and partners with cutting edge molecular breeding technologies and plant trait platforms. For many important agronomical crops, KeyGene has elucidated their highly complex genomes. With its in-house Genome Analysis Platform for the processing of sequencing data, and its proprietary CropPedia interactive platform for big data integration, interpretation, and application, the company has brought crop genomics to a next level. These two platforms create the perfect view on exploitable genetic variation, enabling more efficient use of germplasm and elite breeding materials, and revealing the genetic basis of commercial traits.

    In the partnership with GENALICE, KeyGene was the first company to benchmark GENALICE MAP on agronomic crops. Back in 2012, Prof. Dr. Roeland van Ham, VP Bioinformatics and Modeling at KeyGene, recognized, as one of the first experts in this field, the amazingly high short read alignment speed of GENALICE MAP. He implemented GENALICE MAP as KeyGene’s main NGS secondary analysis pipeline and added Population Calling functionality, which enables KeyGene to process and analyze large cohorts. The software suite currently enables KeyGene to process massive amounts of sequencing data with unparalleled speed and reliability, which is crucial in optimizing and accelerating the molecular breeding process. In the partnership, KeyGene will continue to jointly develop innovative views on genome variation data, and focus on the downstream exploitation of genome data in trait and crop development.” Arjen van Tunen, CEO of KeyGene, comments: “GENALICE and KeyGene are strategically collaborating in a fruitful and mutually profitable way for several years already. I am very pleased with the extension of our partnership which enables both parties to benefit from the further development and use of multi-genome analysis software for AgroFood applications. This will be instrumental for the development of innovative crop varieties that meet future demands for healthy & high quality agricultural products.”

    The GENALICE Vision – an expert’s perspective on high quality, high speed NGS data analysis solutions

    Hans Karten, CEO / CTO of GENALICE, says in a statement: “GENALICE and KeyGene have been collaborating in the space of NGS secondary analysis over the past three years. GENALICE is proud to have played a vital role in KeyGene’s ability to improve their genomic breeding strategies. The advantages of GENALICE MAP core functionality and its Population Calling module have enabled new business opportunities for KeyGene. We are very pleased that this fruitful collaboration is continued by this strategic partnership for the next three years. Again we join efforts in improving plant genomic data analysis and efficiency. The challenges in the food sector continue to increase with stricter health regulations and a fast growing population. This requires the ability to implement innovative approaches, which is a dominant gene in our two companies’ DNA profiles.”

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  • Rollout of GENALICE MAP V2.4.0. on track

    Monday 5 December 2016

    After the initial announcement at the American Society of Human Genetics, in October this year, the GENALICE team is working hard to rollout the new version of the GENALICE MAP NGS secondary data analysis suite, at all of its customer sites. With this new version (V2.4.0) the suite has greatly improved on various elements and expanded with new functional modules.

    In short, the most important updates contain improvements in the basic toolset (Production Box) for single sample short read alignment and variant calling:

    • Further variant detection accuracy improvements; INDEL call optimization
    • Further footprint reduction of unmapped reads, resulting in even smaller GAR file sizes
    • Full GRCh38 support of alternative section/contigs (e.g. distinct haplotypes, decoys) during read mapping
    • HTTPS IO support to be able to run HIPAA compliant
    • HTTP and S3 compatible logging and error report file handles
    • Download of tutorials for training purposes

    Like in earlier versions, V.2.4.0 will give its users access to the GAR toolbox. This toolbox contains the following functionalities:

    • GAR API – providing access to the GAR through C & Java
    • IGV plugin – to view the GAR directly
    • GAR conversion tool (to BAM, SAM and FASTQ)


    The Analysis Suite has been expanded with new functional modules. These modules are considered upgrades; hence they could be added to a standard license for single-sample alignment and variant calling.

    POPULATION CALLING MODULE (already available as an upgrade option within V2.3.0, and now further advanced)
    Advances in the unique Population Calling feature:

    • Profile creation, e.g. a profile can be used as a cohort specific or targeted training set, to better detect known variants. While tools like GATK make use of generic training sets, GENALICE MAP offers users the opportunity to create e.g. race, native population or disease specific profiles. Such a profile allows for target call amplification and suppression, and results in better detection of known variants in the chosen population.
    • Read pileup – The new pileup functionality is a GVM fed read mapping inspection tool. It quantifies coverage depths and variant counts directly from a GAR file.

    A method to distinct variants found in normal tissue from variants in a tumor sample, in order to identify tumor specific DNA mutations. In the Agbio industry, Somatic Calling can also be applied for the identification of new mutations to enhance breeding strategies while finding differentials between a target and base line.

    This newly released Copy Number Variation detection functionality uses a differential approach targeting tumor/normal pairs. Several filters can be applied to surface these areas that have a significant deviation from the expected coverage levels.


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    In case you would like to receive more information about and pricing of our GENALICE MAP NGS secondary data Analysis Suite, please let us know. Just give us a call or send an email us a call or send an email to sales@genalice.com. We are happy to answer all of your questions.

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  • GENALICE expands its NGS secondary analysis suite with important functionality for better diagnosis of oncology patients

    Tuesday 18 October 2016

    Today, at the opening of the Annual Meeting of the American Society of Human Genetics, GENALICE announced the release of a new version (V2.4.0) of its Next-Generation Sequencing (NGS) secondary data analysis suite, GENALICE MAP. The key component of this release is the Somatic Calling module, with impressive performance and best-in-class quality results. Somatic Calling is used for molecular diagnosis of oncology patients. It concerns a technology to distinct variants found in normal tissue from variants in a tumor sample, in order to identify tumor specific DNA mutations.

    In a head-to-head comparison the GENALICE MAP Somatic Calling module outperforms the combination of four commonly used pipelines (MuTect, Strelka, FreeBayes, VarScan), by being 190 times faster and producing better results. None of the individual pipeline results came even close to the results of GENALICE MAP.

    Hans Karten, CEO/CTO, explains: “With the addition of the Somatic Calling module, our NGS secondary analysis solution immediately becomes more relevant for clinical application. The exceptional validation results clearly show our added value in this field. This is an important step forward in realizing the mission of our company to save lives and improve the quality of life of patients with complex DNA diseases, such as cancer.”

    Other important additions to this new software version are:

    1. Profiles: While other tools rely on generic training sets to improve the outcome of known variants in a patient sample, MAP allows for the creation of specific profiles for any defined cohort from no matter what species. Such a profile allows for very targeted call amplification and suppression and thus boosts accuracy of detecting known variants.
    2. Copy Number Variation (CNV): CNV detection, as a first and important element of Structural Variant detection, is now available in GENALICE MAP.
    3. HIPAA compliance: To be able to run HIPAA compliant, hooks to encrypt data in transit and data at rest are provided.
    4. GRCh38 support: Specific support of the ‘alternative sections’ as used in GRCh38 has been added.

    “Another important milestone for our company,” Hans continues, “is the announcement of the first version of our workflow manager. With growing data sets and increasing functionality the need for an excellent system to support smooth big data processing and management in complex environments is clear. The workflow manager delivers full version control and provides a unified view of all samples stored anywhere. The scheduler can work in flex-compute environments and all functionality is accessible through API or Graphical User Interface. We expect this to be an important addition to our product to further reduce the complexity of NGS data processing.”

    For more information on the new Somatic Calling module, please follow this link.


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  • Proceedings PGC Workshop, Presentation GENALICE MAP

    Thursday 12 May 2016

    Executive Summary
    Title: GENALICE MAP – Precision breeding using population Scale Analysis
    Presenter: Hans Karten (CEO/CTO GENALICE)

    GENALICE is a highly innovative bioinformatics big data company. GENALICE designs and builds groundbreaking software solutions for highly accurate, ultra-fast, and cost-effective Next-Generation Sequencing (NGS) data processing and analysis. With GENALICE MAP, the company has built a world-class secondary analysis suite to improve and accelerate molecular breeding. The significant gains are based on smart new algorithms that optimally exploit modern hardware architecture, full potential use of today’s hardware (memory, bus, CPU), and footprint and data stream reduction.

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  • Proceedings PGC Workshop, Presentation KeyGene

    Thursday 12 May 2016

    Executive Summary (on population calling part only)
    Title: Population Calling, Variome analysis and CropPedia to accelerate crop improvement
    Presenter: Alexander Wittenberg (Business Developer Genomics & Genotyping)

    In this presentation an overview was provided of the NGS resequencing projects as ran in daily routine at KeyGene.

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