Bina Bloggers

Video poster hall: An accurate and integrative structural-variant caller

Posted by Jenny Hsu on Oct 8, 2015 9:00:00 AM

Structural variations (SVs) are said to contribute to genomic diversity as well as genomic disorders. Due to their varying lengths, accurate detection of SVs has been challenging with the relatively short-reads generated from next-generation sequencing (NGS). To improve SV detection accuracy and sensitivity, Bina has devised MetaSV, an algorithm that merges results from multiple detection methods. Its overall sensitivity is further enhanced by incorporating a soft-clip based method to boost insertion detection sensitivity.  Watch the following video, where Marghoob Mohiyuddin, our Senior Bioinformatics Scientist and author of MetaSV, presents how the tool improves accuracy of SV calling. Details of the research work is published in Bioinformatics

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Topics: Product, Bina Tools & Workflows, Publication, RAVE, structural variation, MetaSV

VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications

Posted by Jenny Hsu on Oct 1, 2015 11:00:00 AM

Due to the lack of ground truth of real data in high throughput sequencing, simulation methods have been used to assess the accuracy of alignment and variant calling in secondary analysis. In contrast to other tools that generate mutations randomly, VarSim simulates and validates a range of variants based on known SNPs, small indels, and large structural variants, creating synthetic genomes that are biologically relevant. Equipped with interactive statistical reports, it is a robust and comprehensive validation framework for assessing the accuracy of secondary analysis.

Watch the video poster presentation by John Mu, primary author of VarSim. If you would like to learn the details of the methodology, be sure to check out our publication in Bioinformatics, or download our whitepaper.

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Topics: Product, Bina Tools & Workflows, RAVE, VarSim

Conducting a Tumor-Normal Analysis

Posted by Anoop Grewal on Sep 29, 2015 9:00:00 AM

Cancer sequencing analysis represents one of the more complicated NGS workflows. Not only does the typical analysis require identification of variants present in only tumor tissue, the source tissue is often not diploid in nature. Cross contamination of tumor and normal tissue and tumor clonal heterogeneity make variant calling a more significant challenge.

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Topics: Product, Bina Tools & Workflows, RAVE

Analyzing an RNA Sequence in Bina RAVE

Posted by Anoop Grewal on Aug 27, 2015 2:00:00 PM

The Bina Read Alignment, Variant Calling and Expression module, or Bina RAVE, is a software module for secondary NGS analysis that enables fast, accurate, and scalable processing of genomic datasets. In last week's post, we demonstrated tracking and viewing jobs in Bina RAVE. This week, we'll take a look at conducting an RNA sequence analysis.

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Topics: Product, Bina Tools & Workflows, RAVE

CNVkit and Seq2C for Targeted Sequencing

Posted by Li Tai Fang on Aug 25, 2015 12:00:00 PM

To improve detection of copy number aberration (CNA) in targeted sequencing, we have added Seq2C and CNVkit to version 2.6 of the Bina RAVE software module. These tools take advantage of population statistics, with an optional pool of normal controls, to call somatic CNAs in tumor targeted sequencing data.

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Topics: Product, Bina Tools & Workflows, RAVE

Track and View Jobs with Bina RAVE

Posted by Anoop Grewal on Aug 20, 2015 9:00:00 AM

The Bina Read Alignment, Variant Calling and Expression module, or Bina RAVE, is a software module for secondary NGS analysis that enables fast, accurate, and scalable processing of genomic datasets. In last week's post, we demonstrated how easy it is to conduct a DNA whole genome sequence analysis using Bina RAVE. In the video below, we show you how to track and view jobs after a DNA analysis job has been run. 

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Topics: Product, Bina Tools & Workflows, RAVE

Analyze DNA Whole Genome Sequences with Bina RAVE

Posted by Anoop Grewal on Aug 13, 2015 9:30:00 AM

The Bina Read Alignment, Variant Calling and Expression module, or Bina RAVE, is a software module for secondary NGS analysis that enables fast, accurate, and scalable processing of genomic datasets. In the video below, we demonstrate how to conduct a DNA whole genome sequence analysis using Bina RAVE.

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Topics: Product, Bina Tools & Workflows, RAVE

Visualize Filtered Variants in Bina AAiM

Posted by Jenny Hsu on May 5, 2015 9:30:00 AM

In previous videos, we’ve learned how to start a project and query variants in Bina AAiM. In this segment, you will learn how the graphical tools in Bina AAiM can help you quickly visualize annotated variants. Let’s walk through these features in this week’s video.

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Topics: Product, Bina Tools & Workflows, AAiM, Annotation, Videos

The Complexity of Somatic Mutation Detection, and Bina's Solution

Posted by Li Tai Fang on Sep 2, 2014 6:23:00 PM

We have recently released version 2.1 of the Bina genome analysis software, which includes a brand new tumor-normal somatic workflow.

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Topics: Product, Somatic Mutation Detection, Bina Tools & Workflows, Secondary Analysis, Cancer, Tumor-Normal

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