The One Codex Blog

The Brand New One Codex Database has Arrived!

Today we’re pleased to announce the latest update and expansion to the One Codex Database! This update includes the most recent revision of the NCBI taxonomy, improves characterization of complex microbial communities, and increases coverage of species present in the mouse gut microbiome. This release marks our most comprehensive database yet, cataloging over 127,000 genomes across more than 80,000 species. For a comprehensive list of what’s included, check out our references page.

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A Bright Future for One Codex

On behalf of the whole One Codex team, I’m delighted to share that we have spun out One Codex from Invitae as an independent company! I’m extremely grateful to our customers and our team, past and present, for making this transition possible. For everyone who relies on the One Codex platform as the home for their metagenomics research, here are the key points you need to know: The One Codex Platform will continue to be available and operate as-is with no interruptions in service.

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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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