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Downloads and Upgrades: Maverix Biomics, NextCode Exchange, European Variation Archive, and more


Maverix Biomics has added analysis kits for analyzing variants in whole-genome, exome, and targeted resequencing data.

These kits provide open source tools for annotating variants as well as for filtering and interpreting data. Features include the ability to classify hundreds or thousands of samples with unique labels and identifiers including adding phenotypic information to each sample. Users can view their data using the UCSC Genome Browser or in an interactive tabular data visualization tool which lets them sort and filter variants based on multiple parameters. The kits comply with the data management stipulations of the Health Insurance Portability and Accountability Act, Maverix said.

This week, NextCode Health launched the NextCode Exchange, a new genomic data analysis and collaboration service that leverages the company's database architecture and analysis infrastructure.

Clinicians and scientists can use the Exchange in collaborative projects to share sequence data and to validate finds with external colleagues and institutions. Users also control data-sharing settings and can adjust them as they choose by case, project, or institution. It includes tools for users to visualize theirs and collaborators' data and offers access to datasets such as the Simons Simplex Collection (SSC), which comprises genomic sequence and detailed phenotypic data from nearly 2,600 families. NextCode is partnering with the Simons Foundation Autism Research Initiative to make the dataset available for projects focused on autism spectrum disorders.

Current customers of NextCode's system can begin using the Exchange in their studies and collaborations. The list includes clinicians and researchers affiliated with Boston Children's Hospital, University College Dublin, Queensland Institute of Medical Research, and Saitama Medical University among others.

The EMBL European Bioinformatics Institute has launched the European Variation Archive (EVA), a new open source resource that makes it easier to explore genetic variation.

According to the EBI, it is the first archival resource at the institute to provide a single access point for submitting, archiving, and accessing high-resolution variation data of all types. It currently contains data from 15 studies, including the 1000 Genomes project, that collectively describe over 1 billion submitted variants. Users have the option to download data from each study individually or in bulk, and they can search the data by species, projects, chromosomal location, and more. They can also calculate allele frequencies across studies and populations. The resource includes data-mining and visualization tools. To have their data included in EVA, users need to submit a VCF including metadata.

Lab7 System has launched Lab7 Enterprise Sequencing Platform, a new data management solution for next-generation sequencing laboratories, that can be deployed internally or on the cloud.

Features in the software include LIMS lite, a sample tracking and lab communication tool; analysis pipeline creation and management tools that can be integrated with users' existing bioinformatics environment; tools for generating custom reports and visualization capabilities; and more.

Qiagen has added new capabilities to Ingenuity Variant Analysis (IVA) and CLC Cancer Research Workbench.

The company has integrated Biobase's Human Gene Mutation Database with IVA. That means that among other things, users can now utilize ethnicity inference to simplify dataset groupings and to identify variants associated with target traits such as high cholesterol or physical traits. The integration also means that customers of IVA no longer need to purchase separate licenses to HGMD.

CLC Cancer Research Workbench now includes tools to detect copy number variations and variants from RNA-sequencing data. Qiagen has also developed the FastQ-to-insight plug-in, which integrates the Workbench with IVA. The plug-in, which will be released at the end of October, lets users identify and interpret somatic mutations in the Workbench and then analyze and visualize them using IVA.

This week, Genalice officially released Genalice Vault, an all-in-one appliance for next-generation sequence data processing and analysis in genomics studies.

The solution includes workflow management and process monitoring tools, as well as storage space. The appliance is available in various configurations with an increasing number of processing nodes and storage space.

Edico Genome said this week that its Dragen Bio-IT processor is now broadly available to research and clinical laboratories.

The Dragen solution comprises a bioinformatics application-specific integrated circuit, which is embedded on a PCIe form factor card and accompanying software. The solution, which can be integrated into sequencing machines and next-generation sequencing bioinformatics servers, is pre-loaded with optimized algorithms for mapping, alignment, sorting, and variant calling.

Edico first unveiled the solution at this year's Bio-IT World conference.

The bioinformatics group at the University of California, Santa Cruz has released four tracks derived from the dbSNP build 141 data provided by the National Center for Biotechnology Information. The new tracks contain additional annotation data not included in previous dbSNP tracks, with corresponding coloring and filtering options.

GenBank 204.0 is now available via ftp from the NCBI.

Uncompressed 204.0 flatfiles require roughly 680 gigabytes for sequence files only. The ASN.1 data require approximately 557 GB.

Researchers from the Children's Hospital of Eastern Ontario Research Institute and the University of Southampton have developed and released a free software tool called PrimerGenesis that automates primer design for site-directed mutagenesis.

Biomax Informatics has launched version 5.1 of its BioXM Knowledge Management Environment. This version features responsive web design so that it can be used on touch-enabled devices, and a graphical user interface that automatically adapts to the device being used to browse the BioXM portal. It also includes a redesigned ontology module that supports various ontology relations and adds inference and reasoning capabilities; an extended query module; and improved support for third party software.