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上传时间:2018-05-03 10:11:11
Strand Life Sciences announces the release of Strand NGS v3.1 at the world's largest human genetics meeting ASHG 2017, Orlando, USA, 17 -21 Oct 2017. Following Strand NGS v3.0, a DNA-Seq-themed release earlier this year, v3.1 addresses two major themes in NGS: large-scale RNA-Seq data analysis and support for Unique Molecular Identifiers, or UMIs.

Large-scale RNA- and small RNA-Seq support is meant to assist consortium-sized studies in these areas. UMI support will aid the calling of somatic mutations in liquid biopsy and low-grade FFPE samples. Both large-scale-RNA and UMIs are expected to help single-cell RNA studies spanning hundreds of cells.

Large-Scale RNA-Seq Data Analysis:
Strand NGS v3.1 supports the analysis, visualization, and interpretation of RNA- and small RNA-Seq datasets spanning tens of replicates across hundreds of samples. Such large-scale support is expected to help conduct studies involving large populations and multiple cohorts across several population types and several hundred genes of interest. To support large-scale RNA and small RNA-Seq analysis, v3.1 includes the following major workflow enhancements.
• Batch-agnostic confounding variable analysis: With an all-new intuitive interface based on Surrogate Variable Analysis, v3.1 can correct for confounding variables in its RNA-Seq workflow.     
• t-Distributed Stochastic Neighbor Embedding plot (t-SNE) plot: v3.1 includes the t-SNE plot as an alternative to PCA for the visualization and clustering of large numbers of samples.    
• Color scheme: A five-point color scheme generates publication quality plots and a more progressive gradient of color for large number of samples.     
• Sample scalability: Box whisker expression plots change appearance depending on the number of samples being viewed, increasing visual clarity across a large range of samples.     
• Class prediction enhancements: The class prediction workflow can now be reused on an arbitrary number of test datasets across experiments in the same as well as different projects. 
• Gene body coverage plot: Gene body coverage in RNA-Seq can now be visualized as both a heat-map as well as a profile plot.    

Unique Molecular Identifiers: 
Strand NGS v3.1 supports Unique Molecular Identifiers, or UMIs, for DNA-, RNA- and small RNA-Seq. UMIs improve quantification accuracy in RNA-Seq and specificity of low-frequency variant calls in DNA-Seq. In Strand NGS, the UMI feature includes:  
• Robust UMI protocol specification: Strand NGS v3.1 comes with native support for the Rubicon, Qiagen, and Bioos UMI protocols. An intuitive interface also allows the user to specify custom UMI protocols. 
• Exhaustive UMI QC: Several UMI-related QC plots, including the family-size distribution, the percent UMI distribution, and the absolute UMI distribution provide a quick and visual way to verify and validate the UMI workflow.      
• UMI filters: Filters on family size and low frequency families allow the user to exclude poor quality data.     

Apart from these features, Strand NGS v3.1 also consists of a host of minor improvements across all workflows, including VCF import and BAM export enhancements, options for normality testing, and scatter plot improvements. For detailed information, please refer to the release notes.