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We blog about genomics. We also make a platform for open-source analysis of next generation data in the cloud. Hello.

Taxonomic profiling of metagenomics samples: Get to know your loyal residents

Aleksandar Danicic, Nemanja Vucic, Srdjan Kasapovic and Vesna Pajic

Genomics, Science

Numerous colonies of different organisms live virtually everywhere on Earth, even in and on our bodies. They are called microbes and we all know about them. But do we really? Actually, the human race knew nothing about microbes before the 17th century. There were some assumptions and hypotheses, but their

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Differential Methylation Analysis

Milos Nikolic, Tamara Stankovic, Milan Domazet, Sanja Mijalkovic

Science

With few exceptions, every human cell is composed of an identical DNA sequence. However, there are around 200 different cell types in our bodies. What is the underlying reason? Each different cell type represents a specific gene expression pattern. One of the main mechanisms that enables this is epigenetics. Epigenetics

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Optimized Workflow for Bisulfite Sequencing Data Analysis

Vesna Pajic, Tamara Jovanovic, Ana Damljanovic

Science

Epigenetics is an extra layer of information that is not encoded in the primary sequence of an organism’s DNA. While several mechanisms of epigenetic regulation exist, DNA methylation is one of the most commonly studied ones. Typically, the presence of methylated cytosines within a promoter region represses gene expression. The

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3-hour Whole Genome Analysis with GATK4

Vladimir Kovacevic, Teodora Aleksic, Jack DiGiovanna, Stefan Risteski

Science

In the pursuit of accelerating next generation sequencing data processing for clinical applications,  Seven Bridges has developed a configurable GATK4 workflow 3.0 times faster than previous iterations. Following up on our initial push of the GATK4 workflow in 2017, and our recent update with the Broad’s Best Practices, we’ve worked

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Spatial Transcriptomics on the Seven Bridges Platform

Michele Mattioni

Science

As our understanding of biology deepens, many researchers are moving away from bulk gene expression analyses to single-cell analyses. However, current RNA-Seq methods that assay pooled RNA from tissue samples, or even from single cells, fail to conserve the spatial distribution of gene expression within the original tissue. In addition,

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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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We are always engaged in research and development, working to build the future of genomics, science, and health. Let's work together. We'd love to hear about your projects and challenges, so drop us a line.

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