Supporting Memberships for the ATCC Genome Portal
October 9, 2024
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.
Our partnership with ATCC started in 2016 with the launch of the ATCC Microbiome Standards. Ever since, One Codex has been a proud supporter of ATCC and their work driving higher standards of quality in microbial research. As the bioinformatics partner for the ATCC Genome Portal over the last few years, we’re thrilled to share this next step in its evolution.
Below we outline a couple of the key new features we’re launching with ATCC as part of the Supporting Membership program.
The Discrepancy Report
Supporting Members of the ATCC Genome Portal now have access to a new analysis on One Codex called the ATCC Discrepancy Report. One of the most valuable applications of having authenticated genomic data for ATCC’s strains is the ability to compare the biological material you have to the authenticated genomic reference data for that organism.
This will help you catch genomic anomalies in your material early, before they pose a risk to your experiments. The Discrepancy Report is a simple, easy to interpret PDF report that compares your NGS sequencing data to the authenticated ATCC reference genome for the selected organism, and provides you with a set of helpful statistics, including:
- Breadth of genome coverage
- Mean depth of coverage
- Variant calls against the reference genome
- Predicted effect or impact of identified variants
- Detection of divergent or heterogeneous cultures
You can see an example here showing some of the substantial differences between an assembly for an ATCC strain sourced from GenBank compared to the authenticated reference from the ATCC Genome Portal.
Every Supporting Membership includes a number of Discrepancy Reports. Getting started is as easy as launching One Codex and dragging and dropping your FASTQ file of sequencing data - no need to install any software or perform any manual analyses! Here’s a link to our documentation on how to run your first analysis.
And if you don’t have access to a sequencer, you can use our Microbial Isolate Sequencing service and get sequencing data back in 2 weeks!
You’ll be able to learn more about the ATCC Discrepancy Report in an upcoming blog post so make sure to subscribe so you don’t miss out! (Our chat box will pop up with a subscribe option if you’re not already subscribed.)
API Access
Supporting Members also get access to the official REST API for the ATCC Genome Portal. The API gives you programmatic access to all of the data and features in the ATCC Genome Portal. You can search for genomes by metadata or use Sequence Search to identify similar genomes by nucleotide sequence.
Once you’ve identified genomes of interest, you can retrieve the genomic data and genome annotations either in JSON, FASTA, or GenBank (GBK) formats for analysis in downstream workflows.
The ATCC Genome Portal API is a great way to integrate the awesome resources included in the Genome Portal into your workflows and applications. We can’t wait to see how you use it, so if you’ve come up with a creative application for how to integrate ATCC’s genomic data, let us know!
Check out the API documentation to get started with the ATCC Genome Portal REST API.
Group and Institutional Memberships
If you work as part of a research group or institution, you can purchase Supporting Memberships that give your whole team access to the great new features of the ATCC Genome Portal. Easily manage memberships for your team from one place, and effortlessly collaborate and share results from Discrepancy Reports.
As always, the ATCC Genome Portal continues to have a generous free tier that lets you browse and explore the organisms and genomic data in ATCC’s collection. If you have not yet had a chance to check out the ATCC Genome Portal, sign up for an account today at https://genomes.atcc.org.
We’re also working on additional, brand new features and capabilities that will be coming to Supporting Memberships soon. If you have ideas for new tools or resources that you’d like to see, we would love to hear from you!
