The One Codex AmpliSeq™ AMR analysis is compatible with sequencing platforms from Illumina and ThermoFisher (Ion Torrent).

Getting Started

Welcome! You have recently purchased an AmpliSeq™ Antimicrobial Resistance (AMR) Community Research Panel. Now we're going to walk you through using One Codex to analyze next-generation sequencing (NGS) data generated from that panel. Collectively the AmpliSeq™ Antimicrobial Resistance Community Research Panel and One Codex solution will provide you with straightforward analysis of AMR genes for your samples of interest.

Click here to view the above example report.

Register for an Account (if needed)

One Codex is a platform that lets you analyze next generation sequencing data from microbial samples. If you don't have an account, you can sign up for free now.

Just enter some basic contact info, pick a password, and start analyzing data!

Uploading Sample Data

You can add sequencing data generated from the AmpliSeq™ Antimicrobial Resistance Community Research Panel workflow into your One Codex account by navigating to the Upload page, and simply dragging and dropping your FASTQ file(s) directly into the One Codex website.

Don't have a file handy? Feel free to use this FASTQ dataset for the rest of the tutorial: Ampliseq_AMR_Example.fastq.gz.

Need help?

If you get stuck uploading your data into our platform, send us a note using the chat on this page or in the app and we'd be happy to help.

Analyzing your AmpliSeq™ AMR Community Panel data

After you upload your data, you can run the AmpliSeq™ AMR analysis pipeline by visiting the Run Analysis page. Here you can select one or more samples by using the search bar on the left. Once you have a set of samples selected, click "Run" on the AmpliSeq™ AMR Report analysis.

Processing times

Depending on the size of your FASTQ file, you may need to wait a few minutes for these to finish processing.

Accessing your results

On the Sample page for your sample, you can access the analysis by clicking the Analysis dropdown in the top right corner of the page.

For new samples it will be labelled "One Codex Database", which is the default analysis run on every uploaded sample. Below that should be the "AmpliSeq™ AMR Panel", and the "AmpliSeq™ AMR Report". The panel contains the amplicon-level results for each of the amplicons in the panel. The report is a PDF report that aggregates this data into gene-level presence/absence calls for each AMR gene.

An example of the PDF report generated from the AmpliSeq™ AMR Research Panel.


You'll find more details on the bioinformatics behind the AmpliSeq Report here.

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