# 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 Data](https://docs.onecodex.com/en/articles/3764397-importing-data.md): Import data from BaseSpace, or upload through Command Line
- [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 for Ordering Sequencing and Analysis](https://docs.onecodex.com/en/articles/4374804-instructions-for-ordering-sequencing-and-analysis.md): Learn how to order sequencing and analysis for your samples through the One Codex platform
- [Instructions for Registering Samples](https://docs.onecodex.com/en/articles/4378603-instructions-for-registering-samples.md): Learn how to register your samples and submit metadata to ensure your samples get processed correctly
- [Instructions for Reformatting Samples](https://docs.onecodex.com/en/articles/4488002-instructions-for-reformatting-samples.md)
- [Instructions for Packaging and Shipping Samples](https://docs.onecodex.com/en/articles/4384927-instructions-for-packaging-and-shipping-samples.md)
- [FAQ: What is a One Codex Sample Kit?](https://docs.onecodex.com/en/articles/4499901-faq-what-is-a-one-codex-sample-kit.md)
- [FAQ: What kind of samples can I send?](https://docs.onecodex.com/en/articles/4374878-faq-what-kind-of-samples-can-i-send.md)
- [FAQ: Does One Codex sell or recommend specific collection devices?](https://docs.onecodex.com/en/articles/4378991-faq-does-one-codex-sell-or-recommend-specific-collection-devices.md)
- [FAQ: What is a One Codex Reformat Tube?](https://docs.onecodex.com/en/articles/4378962-faq-what-is-a-one-codex-reformat-tube.md)
- [FAQ: How do I use One Codex Reformat Tubes?](https://docs.onecodex.com/en/articles/4378967-faq-how-do-i-use-one-codex-reformat-tubes.md)
- [FAQ: Can I send samples that have already been extracted \(genomic DNA\)?](https://docs.onecodex.com/en/articles/4374885-faq-can-i-send-samples-that-have-already-been-extracted-genomic-dna.md)
- [FAQ: What is the minimum amount of sample I need to send?](https://docs.onecodex.com/en/articles/4378744-faq-what-is-the-minimum-amount-of-sample-i-need-to-send.md)
- [FAQ: How long can I store my samples in One Codex Reformat Tubes?](https://docs.onecodex.com/en/articles/4378970-faq-how-long-can-i-store-my-samples-in-one-codex-reformat-tubes.md)
- [FAQ: What happens to my remaining sample once extraction is complete?](https://docs.onecodex.com/en/articles/4378696-faq-what-happens-to-my-remaining-sample-once-extraction-is-complete.md)
- [FAQ: Do you have a minimum order size?](https://docs.onecodex.com/en/articles/4409199-faq-do-you-have-a-minimum-order-size.md)
- [FAQ: Where is my Barcode ID?](https://docs.onecodex.com/en/articles/4481519-faq-where-is-my-barcode-id.md)
- [FAQ: Can I purchase sequencing and analysis separately?](https://docs.onecodex.com/en/articles/4385434-faq-can-i-purchase-sequencing-and-analysis-separately.md)
- [FAQ: I forgot to register my samples before shipping. What do I do?](https://docs.onecodex.com/en/articles/4378792-faq-i-forgot-to-register-my-samples-before-shipping-what-do-i-do.md)
- [FAQ: I can't find the instructions from my One Codex Sample Kit, what should I do?](https://docs.onecodex.com/en/articles/4499417-faq-i-can-t-find-the-instructions-from-my-one-codex-sample-kit-what-should-i-do.md)
- [FAQ: Can I ship my samples from outside the US?](https://docs.onecodex.com/en/articles/4409179-faq-can-i-ship-my-samples-from-outside-the-us.md)
- [FAQ: When should I expect my package?](https://docs.onecodex.com/en/articles/4374858-faq-when-should-i-expect-my-package.md)
- [FAQ: What do I do if my shipping box is damaged?](https://docs.onecodex.com/en/articles/4378690-faq-what-do-i-do-if-my-shipping-box-is-damaged.md)
- [FAQ: Where do I find my return label tracking number?](https://docs.onecodex.com/en/articles/4378687-faq-where-do-i-find-my-return-label-tracking-number.md)
- [FAQ: Where should I ship my samples to?](https://docs.onecodex.com/en/articles/4374845-faq-where-should-i-ship-my-samples-to.md)
- [FAQ: I've lost my shipping label. What do I do?](https://docs.onecodex.com/en/articles/4378685-faq-i-ve-lost-my-shipping-label-what-do-i-do.md)
- [Sequencing and Analysis Methods](https://docs.onecodex.com/en/articles/6891181-sequencing-and-analysis-methods.md): Include details of our sequencing and analysis in your publication methods section
- [Transnetyx Sequencing and Analysis Methods](https://docs.onecodex.com/en/articles/6891294-transnetyx-sequencing-and-analysis-methods.md): Include details of our sequencing and analysis in your publication methods section
- [FAQ: How do I see the status of my sequencing samples?](https://docs.onecodex.com/en/articles/11322940-faq-how-do-i-see-the-status-of-my-sequencing-samples.md)
- [FAQ: What instruments do you use for sequencing?](https://docs.onecodex.com/en/articles/4409183-faq-what-instruments-do-you-use-for-sequencing.md)
- [FAQ: What kind of controls are used during sample processing and sequencing?](https://docs.onecodex.com/en/articles/4374869-faq-what-kind-of-controls-are-used-during-sample-processing-and-sequencing.md)
- [FAQ: How deep will you sequence my samples?](https://docs.onecodex.com/en/articles/4453190-faq-how-deep-will-you-sequence-my-samples.md)
- [FAQ: How long will it take to get my results?](https://docs.onecodex.com/en/articles/4374856-faq-how-long-will-it-take-to-get-my-results.md)
- [FAQ: How do I download my raw sequencing data?](https://docs.onecodex.com/en/articles/4409189-faq-how-do-i-download-my-raw-sequencing-data.md)
- [FAQ: My sequencing is done. How do I view my results?](https://docs.onecodex.com/en/articles/4374901-faq-my-sequencing-is-done-how-do-i-view-my-results.md)

## Your Authored Workflows on One Codex

- [Introduction to Workflows](https://docs.onecodex.com/en/articles/9922785-introduction-to-workflows.md)
- [Creating Your Workflows](https://docs.onecodex.com/en/articles/9529084-creating-your-workflows.md): A Guide to creating or importing your own workflows on One Codex
- [Dependencies Between Workflows](https://docs.onecodex.com/en/articles/10258650-dependencies-between-workflows.md): Learn how to use the outputs of one workflow as inputs for another.
- [Workflow States and Permissions](https://docs.onecodex.com/en/articles/9554670-workflow-states-and-permissions.md): Learn about the different states a workflow can be in, and what each of those states allow.
- [Launching Your Workflows](https://docs.onecodex.com/en/articles/9519011-launching-your-workflows.md)
- [Setting Workflow Arguments at Launch](https://docs.onecodex.com/en/articles/9554392-setting-workflow-arguments-at-launch.md): Learn how to set your parameters when launching your workflows
- [Viewing Run Details and Results for Workflows](https://docs.onecodex.com/en/articles/9559059-viewing-run-details-and-results-for-workflows.md)
- [GitHub Integration](https://docs.onecodex.com/en/articles/8558569-github-integration.md): Organizations can connect their One Codex accounts directly to their GitHub repositories, to make it easier to run your Workflows
- [Tutorial: Creating and Running a Nextflow Pipeline on One Codex Workflows](https://docs.onecodex.com/en/articles/9922948-tutorial-creating-and-running-a-nextflow-pipeline-on-one-codex-workflows.md)
- [Accessing the One Codex API within Workflows](https://docs.onecodex.com/en/articles/10531998-accessing-the-one-codex-api-within-workflows.md): Learn how to access the One Codex API from within a running workflow

## Kit Guides

- [Getting started with ATCC® Microbiome Standards](https://docs.onecodex.com/en/articles/3754393-getting-started-with-atcc-microbiome-standards.md): How to create an account, upload data from your standards, and view your results
- [Physical product details](https://docs.onecodex.com/en/articles/3754394-physical-product-details.md): Details on all available ATCC® Microbiome Standards \(MSA product line\)
- [Bioinformatics details of ATCC Microbiome Standards](https://docs.onecodex.com/en/articles/3754395-bioinformatics-details-of-atcc-microbiome-standards.md): A detailed description of the bioinformatics workflow used for analyzing your ATCC® standards
- [Bioinformatics Details of the Twist Viral Panels](https://docs.onecodex.com/en/articles/4648676-bioinformatics-details-of-the-twist-viral-panels.md): This guide describes the methods used to analyze data for the Twist Respiratory Virus and Comprehensive Viral Research Panels on One Codex
- [Getting Started with the Twist Comprehensive Virus Research Panel](https://docs.onecodex.com/en/articles/4605793-getting-started-with-the-twist-comprehensive-virus-research-panel.md): This article walks you through uploading an analyzing your first Twist Comprehensive Virus Research Panel samples on the One Codex platform
- [Getting Started with the Twist Respiratory Virus Research Panel](https://docs.onecodex.com/en/articles/4256891-getting-started-with-the-twist-respiratory-virus-research-panel.md): How to create an account, upload data from your Twist Respiratory Virus Research Panel, and view your analyses
- [Getting started with the AmpliSeq™ AMR Panel](https://docs.onecodex.com/en/articles/3754396-getting-started-with-the-ampliseq-amr-panel.md): How to create an account, upload data from your AmpliSeq™ panel, and view your analyses
- [Bioinformatics Details of the AmpliSeq™ Report](https://docs.onecodex.com/en/articles/3764465-bioinformatics-details-of-the-ampliseq-report.md)

## Developer Information

- [API & Client Library](https://docs.onecodex.com/en/articles/3764402-api-client-library.md)
- [Configuring Microsoft Entra ID for Single Sign-On](https://docs.onecodex.com/en/articles/9622857-configuring-microsoft-entra-id-for-single-sign-on.md): This article walks through how to set up a new OAuth2 application in Microsoft Entra ID for Single Sign-On with One Codex

## Technical Appendices

- [One Codex Database](https://docs.onecodex.com/en/articles/3761205-one-codex-database.md): What's behind the One Codex Database
- [Targeted Loci Database](https://docs.onecodex.com/en/articles/3754219-targeted-loci-database.md): Analyzing "barcode" marker genes, such as 16S, ITS, etc. on the One Codex platform
- [Database Versions](https://docs.onecodex.com/en/articles/3764811-database-versions.md): Find a job version ID, and view version release dates

## Advanced Analyses 

- [Custom analysis with Jupyter Notebooks](https://docs.onecodex.com/en/articles/3754220-custom-analysis-with-jupyter-notebooks.md): How to use the built-in Jupyter notebooks functionality for study-level analyses and statistics
- [Coding in Notebooks: A Python Introduction](https://docs.onecodex.com/en/articles/3823135-coding-in-notebooks-a-python-introduction.md): Learn the basics of python coding using Jupyter Notebooks
- [An Introduction to the Jupyter Notebooks Environment](https://docs.onecodex.com/en/articles/3968050-an-introduction-to-the-jupyter-notebooks-environment.md): Learn how to run code using our built-in Jupyter Notebooks
- [Importing and Exporting files with Jupyter notebooks](https://docs.onecodex.com/en/articles/6197530-importing-and-exporting-files-with-jupyter-notebooks.md)

## The ATCC Genome Portal

- [Getting Started with the ATCC Genome Portal](https://docs.onecodex.com/en/articles/3996335-getting-started-with-the-atcc-genome-portal.md): Register for an ATCC account, and see what else you can do in the ATCC Genome Portal
- [Search for a Genome](https://docs.onecodex.com/en/articles/3996699-search-for-a-genome.md): Learn how to restrict your searches to find what you're looking for on the ATCC Genome Portal
- [View Published Genomes](https://docs.onecodex.com/en/articles/3996707-view-published-genomes.md): Understand the information in the table of published genomes on the ATCC Genome Portal
- [The Genome Overview](https://docs.onecodex.com/en/articles/3996705-the-genome-overview.md): Understand the overview tab for a genome on the ATCC Genome Portal
- [View Related Genomes](https://docs.onecodex.com/en/articles/3999534-view-related-genomes.md): Learn how to view genomes related to your genome of interest in the ATCC Genome Portal
- [View Quality Control of a Genome](https://docs.onecodex.com/en/articles/3999565-view-quality-control-of-a-genome.md): Understand the quality control metrics available for each microbe in the ATCC Genome Portal
- [Perform a Sequence Search](https://docs.onecodex.com/en/articles/3999605-perform-a-sequence-search.md): How to perform a sequence search in the ATCC Genome Portal
- [Downloading Omics Data for Purchased ATCC Biomaterials](https://docs.onecodex.com/en/articles/9917786-downloading-omics-data-for-purchased-atcc-biomaterials.md)
- [The ATCC Discrepancy Report](https://docs.onecodex.com/en/articles/9217704-the-atcc-discrepancy-report.md): Learn what the ATCC Discrepancy Report can do for you! Available to Supporting Members.
- [Explore some ATCC genomes](https://docs.onecodex.com/en/articles/10723075-explore-some-atcc-genomes.md)
- [ATCC Genome Portal Technical Documentation](https://docs.onecodex.com/en/articles/3996020-atcc-genome-portal-technical-documentation.md): Learn about the ATCC Genome Portal and our approach to bacterial genome sequencing
- [DNA Extraction](https://docs.onecodex.com/en/articles/3996236-dna-extraction.md): Learn about our approach to DNA Extraction for the ATCC Genome Portal
- [Whole-Genome Sequencing](https://docs.onecodex.com/en/articles/3996240-whole-genome-sequencing.md): Understand ATCC's approach to whole-genome sequencing
- [Genome Assembly](https://docs.onecodex.com/en/articles/3996287-genome-assembly.md): Understand our approach to Genome Assembly for the ATCC Genome Portal
- [Estimation of Genome Relatedness](https://docs.onecodex.com/en/articles/3996311-estimation-of-genome-relatedness.md): ATCC's approach to Estimation of Genome Relatedness
- [ATCC Genome Portal API Guide](https://docs.onecodex.com/en/articles/5812163-atcc-genome-portal-api-guide.md): This provides a guide on how to view, search, and download genomes using ATCC's API
- [Assembly, QC and annotation pipeline versions](https://docs.onecodex.com/en/articles/5357065-assembly-qc-and-annotation-pipeline-versions.md): View the changelogs for the pipelines used to assemble and annotation ATCC genomes
- [How to Cite the ATCC Genome Portal](https://docs.onecodex.com/en/articles/7905448-how-to-cite-the-atcc-genome-portal.md)

## FAQ

- [Q: How do I delete a sample?](https://docs.onecodex.com/en/articles/4136484-q-how-do-i-delete-a-sample.md)
- [Q: How does One Codex work?](https://docs.onecodex.com/en/articles/3770129-q-how-does-one-codex-work.md)
- [Q: What should I expect after uploading data?](https://docs.onecodex.com/en/articles/3770251-q-what-should-i-expect-after-uploading-data.md)
- [Q: How do I set up my payment details?](https://docs.onecodex.com/en/articles/3764266-q-how-do-i-set-up-my-payment-details.md)
- [Q: Can I download read-level results?](https://docs.onecodex.com/en/articles/3770252-q-can-i-download-read-level-results.md)
- [Q: Can I access my results or upload data programatically?](https://docs.onecodex.com/en/articles/3770297-q-can-i-access-my-results-or-upload-data-programatically.md)
- [Q: What happens if my upload includes human reads?](https://docs.onecodex.com/en/articles/3770300-q-what-happens-if-my-upload-includes-human-reads.md)
- [Q: Can I analyze transcriptome/RNA-seq data?](https://docs.onecodex.com/en/articles/3770318-q-can-i-analyze-transcriptome-rna-seq-data.md)
- [Q: Can I analyze 16S or other amplicon \(re-\)sequencing data?](https://docs.onecodex.com/en/articles/3770343-q-can-i-analyze-16s-or-other-amplicon-re-sequencing-data.md)
- [Q: How do I start analyzing my ATCC Microbiome Standard NGS data with One Codex?](https://docs.onecodex.com/en/articles/3770417-q-how-do-i-start-analyzing-my-atcc-microbiome-standard-ngs-data-with-one-codex.md)
- [Q: How do I redeem my coupon code? What happens if I do not receive an email from One Codex with my code?](https://docs.onecodex.com/en/articles/3770437-q-how-do-i-redeem-my-coupon-code-what-happens-if-i-do-not-receive-an-email-from-one-codex-with-my-code.md)
- [Q: Are there more details on the ATCC Microbiome Standards and the bioinformatics analysis?](https://docs.onecodex.com/en/articles/3770444-q-are-there-more-details-on-the-atcc-microbiome-standards-and-the-bioinformatics-analysis.md)
- [Q: Can I share the results of my microbiome sequencing?](https://docs.onecodex.com/en/articles/3770470-q-can-i-share-the-results-of-my-microbiome-sequencing.md)
- [Q: How can I order ATCC Microbiome Standards?](https://docs.onecodex.com/en/articles/3770495-q-how-can-i-order-atcc-microbiome-standards.md)
- [Q: Does One Codex filter or trim sequences?](https://docs.onecodex.com/en/articles/5971379-q-does-one-codex-filter-or-trim-sequences.md)
- [Q: Why are taxonomic results different in the One Codex classification and Functional Analysis taxonomic stratification?](https://docs.onecodex.com/en/articles/6293123-q-why-are-taxonomic-results-different-in-the-one-codex-classification-and-functional-analysis-taxonomic-stratification.md)
- [Q: How do I get the reads that are classified to a specific taxon?](https://docs.onecodex.com/en/articles/5887199-q-how-do-i-get-the-reads-that-are-classified-to-a-specific-taxon.md)
- [Q: How do I cite the One Codex platform?](https://docs.onecodex.com/en/articles/5955982-q-how-do-i-cite-the-one-codex-platform.md)
- [Q: Is One Codex secure?](https://docs.onecodex.com/en/articles/3770560-q-is-one-codex-secure.md)
- [Q: Can I run One Codex on premise?](https://docs.onecodex.com/en/articles/3770597-q-can-i-run-one-codex-on-premise.md)
- [Q: I need another feature. Can I contact you about it?](https://docs.onecodex.com/en/articles/3770610-q-i-need-another-feature-can-i-contact-you-about-it.md)
- [Q: Why is a species considered high-confidence?](https://docs.onecodex.com/en/articles/9875719-q-why-is-a-species-considered-high-confidence.md)
- [Q: What is the difference between "Readcount", "Readcount with children", and "Abundances"?](https://docs.onecodex.com/en/articles/10245796-q-what-is-the-difference-between-readcount-readcount-with-children-and-abundances.md)
- [Q: There are some tags on my sample - what are they?](https://docs.onecodex.com/en/articles/13194381-q-there-are-some-tags-on-my-sample-what-are-they.md)
- [Q: My upload isn't working. What should I try?](https://docs.onecodex.com/en/articles/3770727-q-my-upload-isn-t-working-what-should-i-try.md)
- [Q: I'm having trouble logging in to One Codex. What should I try?](https://docs.onecodex.com/en/articles/3763837-q-i-m-having-trouble-logging-in-to-one-codex-what-should-i-try.md)
- [Q: I've found a bug. How should I tell you about it?](https://docs.onecodex.com/en/articles/3770868-q-i-ve-found-a-bug-how-should-i-tell-you-about-it.md)

## Introduction to the Microbiome

- [Microbiome Overview](https://docs.onecodex.com/en/articles/4136547-microbiome-overview.md): An introduction to the microbiome, and the common terms and analyses used to understand it.
- [Alpha Diversity](https://docs.onecodex.com/en/articles/4136553-alpha-diversity.md): An overview of common alpha diversity metrics for assessing within-sample community diversity.
- [Beta Diversity](https://docs.onecodex.com/en/articles/4150649-beta-diversity.md): An introduction to Beta Diversity, and some of the common ways to measure it.

## Organization Features

- [One Codex Organizations](https://docs.onecodex.com/en/articles/7992919-one-codex-organizations.md)