Blog on One Codex

Updates and improvements to our Targeted Loci Database

Tue, 18 Aug 2026 10:00:00 -0400

We’re proud to announce a major update to our Targeted Loci Database that adds over 19,000 full-length 16S, 18S, and ITS sequences spanning more than 15,000 bacteria, archaea, and fungal species. Additionally, we’ve enriched sequence diversity for over 2,000 exsting organisms, improved accuracy, and made optimizations to maximize species-level detection. With these updates, our Targeted Loci analysis delivers more comprehensive, accurate results, and it’s available now for all One Codex users.

Comprehensive and accurate bacterial isolate characterization using multi-locus sequence typing

Mon, 05 Jan 2026 10:00:00 -0400

We’ve just released an updated MLST analysis that includes improved support for short and long-read sequencing data. In addition to these core improvements, we’ve also expanded our organism coverage to support schemes from over 100 clinically and environmentally relevant species. We hope these updates, which are immediately available to all One Codex users, make it even easier to analyze your isolate sequencing data.

Advancing Viral Metagenomics: Long-Read Support and Customizable Reporting to our Twist Panel Analysis

Wed, 16 Apr 2025 17:00:00 +0000

One Codex’s updated bioinformatics solution for the Twist Viral Panels now supports Oxford Nanopore and PacBio, improves viral detection sensitivity, and offers customizable reporting thresholds to better fit diverse lab workflows.

A new and improved pipeline for detecting antimicrobial resistance markers in metagenomic data

Mon, 10 Mar 2025 10:05:30 -0400

Our new AMR detection workflow is now available and features over 8,500 distinct AMR sequences from 59 drug classes, an order of magnitude more than our previous database! This new workflows covers a wide variety of antimicrobial classes and resistance mechanisms.

Supporting Memberships for the ATCC Genome Portal

Wed, 09 Oct 2024 10:10:00 +0000

As part of our partnership with ATCC, the team at One Codex launched Supporting Memberships for the ATCC Genome Portal earlier this year! In this post we’ll walk through some of the awesome new features and capabilities that Supporting Memberships are bringing to ATCC’s collection of 5000 authenticated microbial genomes. Every quarter ATCC will publish additional genomes.

Automated Drag-and-Drop Microbiome Analysis for Oxford Nanopore Sequencers

Wed, 14 Aug 2024 10:10:00 +0000

We just launched a brand new feature that’s been near the top of the list of requests for a while - now when you want to upload FASTQ files from ONT sequencers but each file is split into several parts we’ll automatically detect the parts and concatenate the files together for you!

Introducing Genome Library

Tue, 06 Feb 2024 17:00:00 +0000

Genome Library is a new feature that simplifies microbial genomics by offering one-click assembly, user-friendly genome annotation browsing, and real-time querying of genomic sequences, addressing challenges in accessing and utilizing genomic data.

Explore your functional microbiome data interactively!

Wed, 15 Nov 2023 10:10:00 +0000

We are constantly looking for new ways to help our users get more out of their data. With many more users exploring Functional Analyses on their samples, we wanted to provide a better way of comparing those results between samples. To kick that mission off, we have now implemented plotting of functional data in our Custom Plots tool!

Detecting novel viral strains with One Codex and Twist Viral Research Panels

Tue, 22 Aug 2023 14:40:00 +0000

Sequencing viral genomes from mixed microbial community samples is challenging due to the relatively low quantity of viral reads compared to host and/or background. One Codex and Twist Bioscience have co-developed targeted enrichment-based sequencing and analysis kits for recovery of whole viral genomes from high-background samples¹. This semi-targeted approach enables enrichment of known viruses while still capturing novel viruses.

The Twist Viral Research panels bundled with One Codex analysis are available in two versions. The Twist Respiratory Viral Research panel covers 29 human and respiratory viral pathogens. The larger Twist Comprehensive Viral Research Panel covers 3,153 viral pathogens known to infect both humans and animals². Both versions have been applied across public health, medicine, academia and industry in diverse use cases, such as evaluating wastewater viromes³, characterization of emerging pathogens⁴, discerning the infectious agent in an outbreak⁵, evaluating co-infections⁶, and novel strain detection^{6, 7}.

One Codex has a new partner: 4bases!

Thu, 20 Jul 2023 06:00:00 -0400

We are excited to announce that One Codex is launching a new partnership with 4bases! 4bases is a Swiss based company with an aim to address unmet medical needs in precision medicine, with clinically-validated and cost-effective solutions for healthcare professionals. One Codex’s mission to enable translational applications of metagenomics and microbiome science strongly aligns with this aim. Notably, this partnership expands One Codex’s reach to European researchers and clinicians.

The 2023 One Codex Database Update

Mon, 10 Jul 2023 10:05:30 -0400

We are thrilled to announce the largest update to our database to date, which now encompasses over 148,000 high-quality reference genomes spanning the entire taxonomic tree. The benefits of increasing the taxonomic breadth of our classifier are multiplied when combined with analytical workflows for microbiome discovery, clinical metagenomics, and genomic epidemiology.

Importing Sequence Read Archive (SRA) Data Into One Codex

Thu, 05 Jan 2023 10:34:30 -0400

We are happy to announce that One Codex now supports importing data from the Sequence Read Archive (SRA), allowing for quick comparison and analysis of publicly available sequencing data and associated metadata.

The Brand New One Codex Database has Arrived!

Mon, 31 Oct 2022 10:34:30 -0400

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.

A Bright Future for One Codex

Wed, 19 Oct 2022 10:34:30 -0400

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.

Improved SARS-CoV-2 Variant Detection with One Codex

Wed, 09 Jun 2021 13:21:55 -0500

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:

Expanding the ATCC Genome Portal With Mycology

Thu, 06 May 2021 09:00:00 -0400

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.

Cataloging the Global Diversity of the Human Gut Microbiome

Mon, 15 Mar 2021 14:41:35 -0400

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.

One Codex is Joining Invitae

Fri, 19 Feb 2021 09:00:00 -0500

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.

Interactive Microbiome Analysis With One Codex

Tue, 19 Jan 2021 09:25:45 -0500

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).

Sample Sizes in Microbiome Research

Tue, 01 Dec 2020 10:28:02 -0500

When you’re planning a new study, there are a lot of factors to consider. These can include:

What population should I target?
How should I collect and store the samples?
What analyte do I want to study, and how should I extract it from the samples?
What kind of technology should I use, PCR, arrays, or sequencing?
What sequencing approach should I use, amplicon or whole shotgun metagenome?
How deeply should I sequence?

These are some common questions researchers ask, and your research goals will drive the decisions you make when setting up your study. But there is a commonly underappreciated question, and one that we at One Codex are often asked: how do I know if I have enough samples?

Five Factors to Consider When Designing a Microbiome Study

Mon, 09 Nov 2020 08:43:46 -0500

Microbiome studies are complex and require up front planning to ensure you get the data you need to answer your research questions. Poor study design can result in missing differences that exist between cohorts, or worse, it can lead to falsely identifying signals that are unrelated to your research questions. Here, we highlight some of the factors to consider when designing a microbiome study to ensure you get the most out of your study.

Introducing Microbiome Sequencing from One Codex

Wed, 28 Oct 2020 13:00:00 -0400

One Codex now offers sequencing! Over the years, we’ve heard the same struggles and frustrations from researchers about their microbiome workflow – slow turnaround times, unpredictable costs, high sample minimums, and data that isn’t as reproducible as it should be. We’re excited to share that we now offer shotgun sequencing, including DNA extraction, library prep, sequencing, and bioinformatics on the One Codex platform. For now, we are focused on stool samples, but stay tuned because there is more to come!

Detecting Respiratory Viruses with Twist and One Codex

Tue, 25 Aug 2020 09:00:00 -0400

Viral metagenomics has become an increasingly important area of study for microbiologists, and it feels especially relevant for 2020 so far. Isolating and sequencing viral DNA or RNA has typically been a tricky and often time-consuming process. We recently partnered with Twist Bioscience to tackle this problem, with the release of the Twist Respiratory Virus Research Panel and One Codex analysis.

ATCC Genome Portal Update: SARS-CoV-2 Genomes and New Support for the ATCC Virus Collection

Mon, 06 Jul 2020 05:00:00 +0000

The One Codex and ATCC teams are working together to support the scientific community during the COVID-19 pandemic by providing reference genomes corresponding to the new authenticated ATCC Coronavirus genomic materials. We’re also working on a whole new virology section in the ATCC Genome Portal with virus-specific features to power your research. In this post, we’ll preview some of these incoming changes to the ATCC Genome Portal and will give you a glimpse of even more new features on their way.

COVID-19 Sequencing Analysis

Mon, 16 Mar 2020 18:59:06 +0000

SARS-CoV-2, the virus responsible for the disease COVID-19, is now widespread within our communities and has personally affected members and friends of our team.

In an effort to contribute however we can, our team has been working to make analysis of genomics data from COVID-19 samples simpler, more accessible, and easier to share with the broader community. Today, we’re announcing a new analysis summarizing the detection of SARS-CoV-2 in samples that contain evidence of the virus. We’re making this analysis available at no charge and it will be automatically run on any samples in which we detect SARS-CoV-2. In return, all that we ask is that you share relevant metadata and the consensus sequences from your samples (and we’ll help enable that).

ATCC Genome Portal Update: Gold Genomes, Tags, and Contig Information

Sun, 01 Mar 2020 05:00:00 +0000

The One Codex and ATCC teams have been hard at work improving the ATCC Genome Portal. Since launching 6 months ago, we’ve more than doubled the number of genomes on the portal (adding more than 300 new genomes on top of our original 250) and created new features to help you navigate our collection of high-quality reference genomes. In this post, we’ll show you our new Gold genomes, help you browse the collection by tag, and show you how to access more granular contig details for each of our genomes.

Publication Highlight: The New Wave of Closing Genomes!

Thu, 13 Feb 2020 05:00:00 +0000

In this post we take a look at a new paper from Eli Moss, Dylan Maghini, and Ami Bhatt that describes a new approach for assembling complete genomes using Oxford Nanopore’s MinION sequencer. Read on to find out more!

A closed genome a day...

Wed, 15 Jan 2020 17:00:00 +0000

The new ATCC Genome Portal offers high-quality, authenticated genomes and annotations for many of the top items in ATCC’s catalog. Today, the portal includes over 365 closed, fully circularized bacterial genomes from ATCC’s collection. That’s 1 genome sequenced and closed per day in 2019! And we’re continuing to generate more data every month.

Growing to more than 100K curated genomes

Thu, 02 May 2019 09:00:00 -0400

The One Codex Database is the most complete, all-in-one microbial genomics database available, and is now more comprehensive than ever! We’re very excited to announce that we’ve just released the latest update to our One Codex Database for shotgun metagenomics, now containing over 40% more curated genomes with 114,505 in total.

What does this mean for you? Your shotgun microbiome analyses are now more accurate than ever, and one analysis provides a complete picture of all of the bacteria, viruses, and fungi in your samples. The One Codex Database lets you quickly and easily characterize everything in your shotgun sequencing data in minutes instead of days.

Interactive microbiome analysis with Jupyter notebooks

Thu, 25 Apr 2019 01:01:01 +0000

We’ve made major updates to our library for fetching, analyzing, and visualizing your One Codex data in a Jupyter notebook. In this post we walk you through a handful of real-world examples of what you can do with these powerful new tools.

SMS-seq 🧬 → ☎️ → 🦠

Mon, 01 Apr 2019 01:01:01 +0000

Announcing SMS-seq: The world’s first protocol for ultra-portable microbial sequencing data analysis and taxonomic identification.

Drag & Drop Your Paired-End Sequencing Data

Fri, 22 Mar 2019 10:24:18 -0700

We heard you! One Codex’s most-requested feature is here. You can now upload your paired-end sequencing data straight from your web browser, and get started with your microbiome analysis faster than ever.

One Codex Achieves Highest Overall Score in precisionFDA CFSAN Challenge 🥇

Wed, 18 Jul 2018 23:29:52 +0000

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:

One Codex Releases New, Largest Ever Database

Thu, 15 Feb 2018 18:54:10 +0000

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. We’ve increased coverage of all branches of the tree of life, with nearly 1,700 fungal genomes, another 1,700 archaeal genomes, 27,000 viruses, and more than 53,000 bacteria. Collectively, this database provides the most comprehensive snapshot of complex microbial samples.

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

Fri, 30 Jun 2017 20:54:31 +0000

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. Today we’re happy to present some results from an independent academic evaluation.² Using the same datasets and accuracy metrics shows the performance of One Codex is superior to a range of other tools for microbiome analysis.

One Codex at ASM Microbe '17

Wed, 31 May 2017 21:23:37 +0000

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. Here will be launching The ATCC® Microbiome Standards powered by One Codex, which are a set of 6 gDNA and whole cell mixed community standards to measure and improve the accuracy and reliability of microbiome sequencing. We will be providing live demos of the platform, including the scorecard analysis of the ATCC Microbiome Standards. For more information about these products, or more, feel free to email us.

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

Tue, 04 Apr 2017 00:23:29 +0000

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.

Notebooks (and more!)

Thu, 10 Nov 2016 19:51:52 +0000

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!

The new Notebooks feature allows you to launch secure Jupyter (née IPython) notebooks automatically configured for access to your samples and analyses on One Codex. Internally, we’ve already found these incredibly useful for both quick, flexible explorations of metagenomic data as well as more sophisticated, formal analyses.

Running new analyses & whole-genome alignments

Mon, 26 Sep 2016 17:53:27 +0000

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. While in the past we’ve configured additional analyses to run automatically where appropriate (e.g., MLST for common bacterial isolates) or at the request of users, our new Run Analysis page allows you to run an in silico panel or perform whole-genome alignments against any of your samples.

Detecting Antimicrobial Resistance in Foodborne Pathogens

Thu, 18 Aug 2016 16:37:00 +0000

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. Both E. coli and C. coli / C. jejuni are dangerous foodborne pathogens that can be highly resistant to antibiotics. These panels are designed to help microbiologists use genomic sequencing to track the spread of foodborne illness, and predict what antibiotics may not be effective for treating these pathogens.

2.0!

Mon, 25 Apr 2016 18:30:37 +0000

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. These methods have enabled ever-larger reference libraries and provided extremely sensitive detection. As a consequence of their design, however, they have also been more prone to false positives than more conservative alignment- or marker-based approaches.

New features: Whole genome clustering and BaseSpace integration

Thu, 11 Feb 2016 21:08:49 +0000

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. This cluster view (login/free registration required) enables rapid, reference-free exploration and comparison of NGS samples, often both highlighting expected similarities and revealing important inter-sample differences.

Cautious Metagenomics: A Story of Anthrax in the NYC Subway

Mon, 11 Jan 2016 15:36:00 +0000

Ok, anthrax might sound a bit scary, but this is a story about something that should make you feel good.

Wait, is that really Anthrax?

Back in the Spring of 2015, researchers studying the microbial ecology of the built environment generated a very large amount of genomic data from microbes found in the New York City subway system. To give you some idea of the magnitude, they generated 10.4 billion sequence reads across 1,457 samples. That’s a lot of microbiome data.

Automated MLST annotation

Tue, 10 Nov 2015 23:51:59 +0000

Today we added automated Multi-Locus Sequence Typing (MLST) to One Codex.

MLST is a powerful epidemiological tool that is based on curated collections of conserved mutations in core marker genes. This common reference standard is used to differentiate closely-related isolates of the same species, with many common species having hundreds or thousands of defined MLST profiles.

Datasets that are identified as being isolates or single-genome assemblies will be automatically analyzed and tagged with the detected ST label. This MLST tagging is implemented for the most commonly analyzed bacteria, including E. coli, S. enterica, and L. monocytogenes.¹

Launching out of beta!

Thu, 22 Oct 2015 14:40:00 +0000

Today is a big day for One Codex, where we’re launching out of beta!

This marks the introduction of a number of new features (and many under-the-hood improvements), and incorporates much of the feedback our users have provided this year. You will notice some changes to our website, and the platform can now be found at app.onecodex.com (note that all previous links to the beta site will still work).

Sample comparison tool

Mon, 27 Apr 2015 20:08:10 +0000

Today we’re launching our new sample comparison tool on the One Codex Beta Platform.

The tool enables quick selection and comparison of any of your samples and displays the abundance of taxonomic groups in each sample as a stacked bar graph:

The comparison view supports large side-by-side comparisons, viewing data at a particular taxonomic level and/or abundance, filtering to specific clades, and relative vs. absolute scaling modes.

See an example and try out the tool here

Instant sequence search

Thu, 19 Mar 2015 22:39:07 +0000

We’re pleased to announce that we’re launching a new feature on One Codex today: instant sequence search.

With this new tool, simply enter a nucleotide sequence – whether a read from a FASTQ file or a section of a reference genome – and we’ll instantly compare it against our One Codex database.

How it works

Our instant classifier works by splitting up the input sequence into all overlapping k-mers and then comparing each against our reference database, using a k=31. We then visually highlight the most specific taxonomic value (or lowest common ancestor) for the k-mer in our database. (Note that because the k-mers overlap, we only color the first character of each)

Larger, improved reference libraries

Fri, 06 Mar 2015 21:50:12 +0000

We’re happy to announce that we’ve just released larger, improved microbial reference libraries on One Codex.

More data

The RefSeq Database now includes over 7,000 reference and representative genomes from NCBI, while the One Codex Database holds nearly 34,000 different bacterial, viral, fungal, and archeal genomes. This is more than a 45% and 20% increase, respectively, from the last releases of the RefSeq and One Codex databases. As with all of our data releases, you should continue to see improvements in the specificity of your analyses by using our more comprehensive reference libraries.

Public links and a better datasets view

Tue, 03 Feb 2015 00:17:35 +0000

This week, we’re excited to announce a few improvements to help you to better organize and share your data on the One Codex beta platform.

First, you can now make individual samples public, at which point you can share an analysis with anyone (and, of course, you’re always able to make the sample private again too). Here’s a sample public analysis.

Second, we’ve added the ability to both sort and filter your samples in the main datasets view. This is particularly useful for some of our users who are beginning to accumulate large numbers of samples.

CDC "No-Petri-Dish" Challenge

Mon, 26 Jan 2015 18:16:59 +0000

We’re excited to announce that the CDC’s Advanced Molecular Detection initiative has named One Codex as the winner of its $200K “No-Petri-Dish” Challenge! We are thrilled to be recognized by a world-leading public health agency and excited to begin offering solutions for next-generation public health and epidemiology.

The “No-Petri-Dish” Diagnostic Test Challenge asked participants to develop a fast “straight-to-strain” method for identifying a type of E. coli known as STEC (a common cause of severe foodborne outbreaks). Current tests available to public health officials fall into two major categories: “culture-based” tests, which require growing a bacterial culture and can take days or weeks to complete; and faster, but significantly less informative tests for specific pathogens or toxins (e.g., PCR-based tests).