The One Codex Blog

One Codex Achieves Highest Overall Score in precisionFDA CFSAN Challenge 🥇

One Codex Team on  July 18, 2018
preview , strains , Benchmarking , precisionFDA

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

One Codex Team on  February 15, 2018
reference data , announcements , microbiome

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

One Codex Team on  June 30, 2017
metagenomics , microbiome , Benchmarking

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

kashef qaadri on  May 31, 2017

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

Sam Minot on  April 4, 2017
new features , reference data , 16S , 18S , ITS , 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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