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Downloads and Upgrades: GATK 2013.1, Reaxys, Vector NTI Express Designer, and more

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Appistry has launched the first fully supported commercial release of the Genome Analysis Toolkit.

Version 2013.1 includes all the updates, enhancements, and issue resolutions made by the Broad Institute since a preliminary commercial release from Appistry last December. Features include base quality score recalibration, which provides a calibrated error model from which to make mutation calls and is better at modeling small NGS sample sizes; faster versions of the Unified Genotyper and the Haplotype Caller; and new and expanded tools for filtering data types, tabulating concordance results, refreshing genotype information in VCF files, and combining non-overlapping VCF files among other updates.

Appistry also announced this week that it is making the source code to the GATK available to customers to enable them to develop tools on top of the engine and integrate the GATK into their NGS systems, programs, and workflows. Access to the source code is provided as part of every enterprise GATK license from Appistry. Users holding lab, workgroup, or single-user licenses may purchase access to the source code for an additional fee.


This week, Elsevier announced that it has included additional content and launched an improved user interface for Reaxys, its chemistry workflow solution.

The added content means that Reaxys now encompasses over 16,000 periodicals and covers 30 million reactions and over 500 million experimentally measured data.


Life Technologies has launched Vector NTI Express Designer, an added feature to its Vector NTI software platform, which provides researchers with tools for custom vector and genetic construct design and synthesis.

According to the company, Express Designer has an integrated gene synthesis service which lets users submit sequences quickly and place orders. Customers can also use the tool to design custom DNA parts and submit them directly to Life Technologies' GeneArt portal for synthesis. It also lets users fine tune expression levels of cloned genes; enables construction of multiple vectors for compatible and simultaneous function; and generates variants from template DNA parts, devices, and circuits among other capabilities.


Cufflinks 2.1.0 is available here.

This release includes improvements in the accuracy, speed, and memory footprint of Cufflinks and Cuffdiff. Other changes include several bug fixes, a new statistical test for Cuffdiff, and an optimized sampling procedure that improves the running time for Cuffdiff among other updates.


Ensembl 71 is available here.

The release includes new SIFT scores for all possible changes to the proteome in human, mouse, zebrafish, pig, cow, chicken, rat and dog; new views and web features including a new clinically associated summary track on Region in Detail for human variation; and updated gene sets from human, zebrafish, and Anole lizard among other updates.


The genome browser group at the University of California, Santa Cruz has remodeled the interface of the Cancer Genomics Browser to make it easier to navigate, display and analyze data.


Filed under

The Scan

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.

Family Genetic Risk Score Linked to Diagnostic Trajectory in Psychiatric Disorders

Researchers in JAMA Psychiatry find ties between high or low family genetic risk scores and diagnostic stability or change in four major psychiatric disorders over time.

Study Questions Existence of Fetal Microbiome

A study appearing in Nature this week suggests that the reported fetal microbiome might be the result of sample contamination.

Fruit Fly Study Explores Gut Microbiome Effects on Circadian Rhythm

With gut microbiome and gene expression experiments, researchers in PNAS see signs that the microbiome contributes to circadian rhythm synchronicity and stability in fruit flies.