The One Codex Blog

One Codex Achieves Highest Overall Score in precisionFDA CFSAN Challenge 🥇

Identifying specific strains and mixtures of strains in complex metagenomic samples is a key challenge in epidemiology, environmental microbiology, and live biotherapeutics development (LBPs). We’ve long been working on this problem and are excited to announce that our in-house strain-calling pipeline recently achieved the highest overall score in the precisionFDA CFSAN Pathogen Detection Challenge. We’re still continuing to hone and test several approaches, but are excited to see that each performed extremely well across the 25+ submissions:

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One Codex Releases New, Largest Ever Database

Today at the Advances in Genome Biology & Technology (AGBT) conference, we are excited to unveil the largest searchable database of microbial genomes. Curated from its larger collection of hundreds of thousands of genomes, the latest One Codex Database includes >80,000 genomes and provides unprecedented sensitivity and specificity for metagenomic applications. The latest One Codex Database enables: Highly sensitive identification of microbes in complex samples Precise quantification of microbial abundances from whole genome sequencing (WGS) data Community-wide characterization of complex microbial samples, including the human microbiome Spanning the tree of life Our latest release includes over 80,000 genomes, representing more than 43,000 distinct species and 69,000 strains across all microbial domains.

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Academic Study Data Shows One Codex’s Superior Performance for Metagenomic Analysis

When analyzing microbiome data, it’s very important to know that you are detecting the microbes that are truly present and that the predicted abundances are accurate.1 However, it can be a lot of work to test and validate microbiome analysis tools across a wide range of conditions. We are very grateful to a group of academic researchers from Weill Cornell Medicine, UC-Riverside, IBM, University of Vermont, HudsonAlpha, & Drexel University who performed those evaluations and contributed them to the community.

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One Codex at ASM Microbe '17

ASM Microbe, one of the largest microbiology conferences in the world, is right around the corner. With more than 10,000 attendees, it’s a great event to connect with the research community, learn the latest scientific advances, and introduce microbial genomics experts to the One Codex platform you have come to love. If you are attending the conference, please stop by ATCC’s booths (#2411 & 2413) to meet the One Codex team or send us a note.

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Announcing the Targeted Loci Database for 16S and other amplicon sequencing

Scientists that study the microbiome generally use two different methods to analyze samples – sequencing all of the DNA in a sample (whole genome sequencing) or targeting a specific marker gene (e.g., 16S, 18S, ITS). While whole genome sequencing (WGS) enables high-resolution taxonomic and functional characterization of microbiome samples, 16S sequencing is a cost effective technique for broad community surveys across large numbers of samples. Today, we’re excited to announce that One Codex is launching a powerful new tool for 16S and other amplicon sequencing – making high-quality, reference-based analysis of marker gene studies easier, faster, and more accessible.

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Notebooks (and more!)

Today, we’re extremely excited to announce several new features we’ve been working on for the past few months. Collectively, these should make it both easier and faster to perform custom, large-scale analyses, explore your data, and build applications atop the One Codex platform: A new easier-to-use, more powerful API (read the docs) A new version of our command-line interface and an accompanying Python client library for quickly getting started with the new API (take a peek on Github) And last but not least – interactive notebooks built directly into the platform!

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Running new analyses & whole-genome alignments

Today we’d like to tell you about a new feature on One Codex that allows you to run new analyses against your samples, including AMR gene panels and whole-genome alignments. Running New Analyses When samples are uploaded to One Codex, we automatically classify them using the One Codex Database of ~40K complete microbial genomes. However, metagenomic classification is just one of a range of microbial analysis tools provided by the One Codex platform.

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Detecting Antimicrobial Resistance in Foodborne Pathogens

Today we’d like to tell you about a set of panels on One Codex designed to help detect antimicrobial resistance (AMR) in two important foodborne pathogens – Escherichia coli and Campylobacter coli / C. jejuni. AMR in E. coli and Campylobacter coli / C. jejuni Antibiotic resistant infections are a huge challenge for modern healthcare, and there is a global effort underway to improve our identification and treatment of these hardy infections.

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2.0!

Today we’re excited to announce a major update to One Codex, which includes both improvements to our core metagenomics pipeline and an expansion of our reference database. Along with this update, we’ve also re-analyzed all samples previously uploaded to One Codex (all older analyses of course remain available). Improved classifier: Better filtering, while maintaining sensitivity Over the past few years, a number of new k-mer based metagenomic classifiers tools have been developed, including Kraken, GOTTCHA, CLARK, and our own.

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New features: Whole genome clustering and BaseSpace integration

Today we’re happy to announce two new features for all users on One Codex: whole genome clustering and integration with Illumina’s BaseSpace. The first opens the door to new types of analyses, while we hope the second will allow many to spend less time moving their data around and more time exploring it! Whole (meta)genome clustering In addition to our previous sample comparison tool, we’re very excited to announce that One Codex now supports arbitrary, interactive exploration and clustering of your isolates and metagenomic samples.

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