The One Codex Blog

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.

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.
• The majority of the One Codex team has decided to join the new company and is committed to ensuring the success of the platform and our customers. Many of these folks have been with us for 2+ years, even before we joined Invitae. We’re also excited to welcome a couple of new team members that joined us last year at Invitae!
• An important part of this process has been maintaining a strong strategic relationship with Invitae for lab services, letting us continue to support our customers with rapid and flexible shotgun microbiome sequencing and analysis.
• Importantly, there will be no changes to the sequencing workflow, so you can count on the same quick turn-around time and quality for sequencing data.

For those considering One Codex for your upcoming microbiome sequencing projects, this means we will continue to have the flexibility and scalability required to support our rapid, cost effective microbiome sequencing program to the same high standard as always. For customers who have worked with us previously, it means there are no changes to the data generation workflow that could otherwise introduce risk or technical variability into your data.

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. The pipeline now deals exclusively with tiling amplicon data generated by ARTIC V3 protocols, which have been widely adopted for detecting SARS-CoV-2 variants. The pipeline takes in either Oxford Nanopore or Illumina FASTQ data and processes them as follows:

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. Nevertheless, we are excited to provide researchers with our small but growing collection of ATCC mycology genomes.

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). Science is still trying to answer the question of who lives in our guts, what differences exist between people, and the underlying mechanisms behind these differences.