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One Codex Docs
Guides and documentation for using One Codex
- Authority
- 46 reach 0 · trust 10 · quality 21 · freshness 15
- Tier
- listed
- llms.txt
- https://docs.onecodex.com/llms.txt
- Sections
- 13
- Links
- 131
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- Registered
- 2014-07-10
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- For agents
- Documentation: developer or product docs worth reading, nothing to call
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Their llms.txt
The beginning of the file, from our validated copy saved 2026-10-25T23:27:37.174Z. Cached copy · Source on onecodex.com
# One Codex Docs
> Guides and documentation for using One Codex
## Introduction
- [Getting Started](https://docs.onecodex.com/en/articles/3743223-getting-started.md): How to register for an account, upload samples, and analyze and compare your results
- [Core Concepts](https://docs.onecodex.com/en/articles/3764252-core-concepts.md): Working with your samples, metadata, and analyses on One Codex
## Sample Management
- [Sample Management](https://docs.onecodex.com/en/articles/3764578-sample-management.md): Viewing, organizing, and searching your samples across One Codex
- [Metadata](https://docs.onecodex.com/en/articles/3764349-metadata.md): Add metadata to your samples to enable group searching and extra analyses
- [Importing/Uploading Data](https://docs.onecodex.com/en/articles/3764397-importing-uploading-data.md): Learn how to upload your files, or import data from BaseSpace or the SRA
- [Sharing & Projects](https://docs.onecodex.com/en/articles/3764345-sharing-projects.md): Group your samples into Projects, and share with your collaborators
## Analyses
- [COVID-19 Sequencing Analysis](https://docs.onecodex.com/en/articles/3793936-covid-19-sequencing-analysis.md): Test your samples for SARS-CoV-2
- [Metagenomic classification](https://docs.onecodex.com/en/articles/3753847-metagenomic-classification.md): Analyzing whole genome sequencing \(WGS\) and targeted sequencing \(e.g., 16S\) data on One Codex
- [Panels](https://docs.onecodex.com/en/articles/3753767-panels.md): Evaluating the presence of anti-microbial resistance \(AMR\) genes, virulence factors, and other functional markers
- [Functional Analysis](https://docs.onecodex.com/en/articles/6293070-functional-analysis.md): Describes the Functional Analysis and how it works, giving a walkthrough of the resulting report.
- [One Codex Alignments](https://docs.onecodex.com/en/articles/6330105-one-codex-alignments.md): An Introduction to One Codex Alignments, and How to Run Them
- [Running Analyses on One Codex](https://docs.onecodex.com/en/articles/9557729-running-analyses-on-one-codex.md)
- [Switching Between Analyses for a Sample](https://docs.onecodex.com/en/articles/9573180-switching-between-analyses-for-a-sample.md): Use the dropdown menu to view different analyses
- [Multi-Locus Sequence Typing \(MLST\) on One Codex](https://docs.onecodex.com/en/articles/13185192-multi-locus-sequence-typing-mlst-on-one-codex.md)
- [Compare Abundances with Quick Compare](https://docs.onecodex.com/en/articles/4789397-compare-abundances-with-quick-compare.md)
- [Visualizing microbiome data with Custom Plots](https://docs.onecodex.com/en/articles/4633959-visualizing-microbiome-data-with-custom-plots.md): Learn how to compare samples and make common microbiome plots on the One Codex Platform
- [Exporting Results Tables](https://docs.onecodex.com/en/articles/5941871-exporting-results-tables.md): Easily download excel tables of your classification data
## Microbiome Sequencing and Analysis
- [Instructions f
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