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Smart Variant Filtering

Vladimir Kovacevic

Science

The variant filtering process consists of selecting highly confident variants and removing the ones that are falsely called. Secondary genomic DNA analysis is mainly oriented toward alignment and variant calling, assuming the accuracy of these two would provide major influence on the overall quality. The variant filtering step used to

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Circulating Tumor DNA Analysis on the Seven Bridges Platform

Sanja Mijalkovic, Luka Topalovic, Ognjen Milicevic

Science

Next Generation Sequencing (NGS) has brought significant improvements in all areas of biotechnology and healthcare — and cancer screening is no exception. The latest game-changer is liquid biopsy, a novel and challenging NGS application. By directly measuring and analyzing circulating tumor DNA (ctDNA) in blood, liquid biopsy is a promising,

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The GA4GH Workflow Execution Challenge: evaluating reproducibility and portability across platforms

Guest Author: Brian O’Connor

Science

Large-scale, geographically distributed genomics analysis efforts, such as the PanCancer Analysis of Whole Genomes (PCAWG) project, highlight a trend in our community towards moving compute to where data resides. For PCAWG, this was out of necessity as the genomes for ~2,800 cancer donors were stored across 8 different locations around

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Sequence Bloom Trees, Part I: Motivation and principles

Nate

Science

Modern bioinformatics involves a lot of searching datasets, like The Cancer Genome Atlas (TCGA), that contain data from many experiments. Wanting to do this efficiently raises not only data management problems but also algorithmic ones. Searching a dataset like TCGA in hopes of figuring out which experiments contain a given

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Identifying viral sequences in TCGA data using Kraken and Centrifuge

Patrick

Genomics, Science

Image adapted from Kim et al. Genome Res. 26, 1721–1729 (2016). Next-Generation Sequencing has opened up the field of metagenomics. In metagenomic studies, a sample often contains a complex ecosystem of different microorganisms. The key challenge in these experiments is disentangling the identities of unknown species from millions of sequencing reads. Bioinformatic tools for metagenomics are designed to

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Festival of Genomics: Reflecting on graph genomes

Nick

Graph Genome, Science

Yesterday at Festival of Genomics, London, Seven Bridges CEO Deniz Kural joined a panel discussing implementations of graph genomes, alongside Erik Garrison from the Wellcome Trust Sanger Institute and Andy Yates from EMBL-EBI. Great panel talking about #graph #genomes at #GenomicsFest @erikgarrison @denizkural Andrew Yates @FLGenomics pic.twitter.com/4Cxy2CslvT — Adrian Alexa

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Bioinformatics applications in cancer immunotherapy

Jessica Lau

Science

An emerging characteristic, or hallmark, of cancer cells is their ability to evade destruction by the immune system. While immune surveillance plays a role in controlling tumorigenesis and tumor progression, cancer cells can in turn disable the immune system by secreting immunosuppressive factors or recruiting immunosuppressive cells. Because of this

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The race for a revolutionary new cancer diagnosis tool: The Blood Profiling Atlas in Cancer

Patrick

Blood Profiling, Cancer Moonshot, Science, Useful Data

A revolutionary approach to cancer diagnosis Liquid biopsy, a new technique for tracking down fragments of tumor DNA in the blood, has the potential to revolutionize how cancer is diagnosed and treated. At next week’s Precision Medicine World Congress, Seven Bridges’ Bruce Press will lead the “Update on the Cancer

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