The One Codex Blog

Improved SARS-CoV-2 Variant Detection with One Codex

In March of 2020, a few weeks after the WHO declared a global COVID-19 pandemic, One Codex released a free, publicly available pipeline for processing different types of SARS-CoV-2 sequencing data (WGS, amplicon, hybrid capture). This pipeline is automatically run on any One Codex sample in which SARS-CoV-2 is detected, and is part of our effort to contribute what we can towards the public health response. We’re happy to announce that One Codex has now updated our SARS-CoV-2 pipeline with additional and improved features that reflect the changing nature of the pandemic.

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Expanding the ATCC Genome Portal With Mycology

We teased a few months (blogs) back that we were working on fungal data. We are excited to finally announce the addition of reference-quality genomes from our mycology collection to the ATCC Genome Portal. The addition of fungal genomes to the ATCC Genome Portal was a significant step for us. Extracting high-quality, concentrated gDNA from fungi is often more complicated than extracting similar quality gDNA from bacteria or viruses. Significantly larger genomes are less compatible with higher throughput sequencing technologies than the smaller viral genomes.

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Cataloging the Global Diversity of the Human Gut Microbiome

The microbial communities that inhabit our bodies can be thought of as unique fingerprints that both reflect and help determine many aspects of our health. Currently, metagenomic sequencing offers the best window we have into our microbiomes, which are primarily composed of uncultivated organisms. However, despite important insights gained from 20+ years of sequencing human microbiomes, it is estimated that 40-50% of species in the human gut microbiome lack reference genomes (Nayfach et al, 2019, Nature).

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One Codex is Joining Invitae

At One Codex our mission is to support and advance microbiome discovery through accurate, scalable, and easy-to-use software. By giving scientists better leverage over their genomics data, we’ve helped to accelerate programs in basic and translational research, infectious disease diagnostics, and therapeutics development. I’m thrilled to announce that One Codex has been acquired by Invitae, where our full team will continue our work to make microbiome data more reproducible, more accessible, and ultimately translatable to clinical practice.

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Interactive Microbiome Analysis With One Codex

Today, we’re very excited to launch a brand new feature on One Codex that lets you analyze your microbiome data in all new and exciting ways! Custom Plots is a powerful new application for interactively comparing and visualizing your microbiome data across cohorts of many samples. With Custom Plots, you can explore a variety of different microbiome metrics and plots that were previously only accessible through our Notebooks. This includes taxonomic bar charts (like our current “Quick Compare” tool), alpha diversity plots, and beta diversity plots like heatmaps or Principal Coordinate Analyses (PCoA).

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