Bina Bloggers

2015: A Big Year for Bina

Posted by Jenny Hsu on Dec 17, 2015 1:50:16 PM

This year zoomed by at Bina! We’ve grown tremendously and bagged several major accomplishments. Here are a couple of highlights from 2015:

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Topics: News, Publication, Bina Alliance Program, Bina

Gold Standard Genome for Validating Structural Variant Calling Methods

Posted by Jenny Hsu on Nov 11, 2015 9:00:00 AM

A high-confidence, comprehensive human variant set is crucial for assessing the accuracy and quality of sequencing algorithms, particularly for use in precision medicine. Despite recent research efforts, an all-encompassing variant call set including structural variants (SVs) is still lacking.

In the following poster presentation, our Research Engineer, John Mu, details the construction procedure of a real data validation set leveraging reads from the Venter genome and others. This gold set includes small variants, as well as deletion SVs and insertion SVs up to 100K base-pairs. 

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Topics: Bina Tools & Workflows, Publication

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

BreakSeq2: Improved Nucleotide-Resolution Analysis of Structural Variants

Posted by Marghoob Mohiyuddin on Aug 6, 2015 10:02:00 AM

Junction-mapping or the related split-read analysis is a popular method for detecting structural variations (SVs), which are large variations in the genome. SVs have been implicated in various genomic disorders and are key to understanding the genomic diversity. Junction-mapping relies on mapping short reads to known breakpoint sequences in order to detect SVs.

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Topics: Bioinformatics, Publication, structural variation

MetaSV: An Accurate and Integrative Structural-Variant Caller for Next-Generation Sequencing

Posted by Jenny Hsu on May 12, 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).

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Topics: Publication, structural variation

A High-Fidelity Simulation and Validation Framework for High-Throughput NGS

Posted by John Mu on Feb 10, 2015 1:41:00 PM

We are excited to introduce VarSim, a comprehensive tool for the validation of secondary analysis in high throughput sequencing. It assesses both alignment and variant calling accuracy through a simulation that is based on real experimental data, and is capable of handling a wide range of variants, including single nucleotide variants, small indels and large structural variants.

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Topics: Whitepaper, Secondary Analysis, Validation, Publication

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