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For detailed instructions on using our API please go here: [https://github.com/CosmosID/cosmosid-cli/blob/master/README.rst](https://github.com/CosmosID/cosmosid-cli/blob/master/README.rst)

API Documentation

Cosmosid

The Leading Cloud-Based Microbiome Analysis Platform

About the Cosmos-Hub

An overview of how to get started with Cosmos-Hub and our award winning pipelines.

Quickstart

Setting up your account

The Cosmos-Hub can import raw FASTQ data shotgun and amplicon metagenomic sequencing for taxonomic and functional analysis.

Uploading Sequencing Data

Cosmos-Hub streamlines the process of organizing and analyzing your microbiome data by linking it to relevant experimental or sample metadata. Follow these detailed instructions to ensure smooth and efficient metadata integration into your analysis workflows.

Uploading Metadata

This page describes each of the workflows available in the Cosmos-Hub.

Available Data Workflows

Create Comparative Analysis

The Cosmos-Hub allows you to store and download your raw fastqs/sequencing data from the dashboard.

Raw Data Download

View, rename, create folders and move your samples using the sample dashboard

Organize Your Data

You can download your sample results files as well as visualizations and comparative analysis results. 

Download Your Results

Viewing Single Sample Profiling Data

The sample abundance table is the main page for viewing individual samples.

Sample Abundance Table

Sunburst

Bubble Graph

Collapsible Tree

Radial Tree

Donut Graph

Stacked Bar Graph

Combined Kingdom Analysis

FASTQC

Filtering

(Meta)Transcriptomic Analysis in the HUB

Overview

View

Matrix Table

CosmosID's heat map visualizes comparative analysis results using a red-to-blue color spectrum, where red indicates high values and blue represents low values.

Heatmap

Abundance Distribution module allows you to visualize the distribution of individual taxa/features using boxplot across your chosen cohorts.

Abundance Distribution

Principal Component Analysis (PCA) is used to visually explore complex data in a way that makes it easier to emphasize variation to bring out strong patterns.

Alpha diversity is a fundamental concept in microbiome analysis, measuring the variety of species within a single sample.

Alpha Diversity

Beta diversity is a fundamental concept in microbiome analysis that measures the differences in species composition between multiple samples or cohorts, providing insight into the variation across different environments or conditions.

Beta Diversity

The number of reads in each sample compared on a graph.

Read Statistics

LEfSe Biomarker Discovery Analysis

MaAsLin2 for Differential Abundance

We recommend running MaAsLin analyses independent of other comparative analyses. Once the parameters are set, click the Create button to start the MaAsLin2 workflow. CosmosID-HUB will process the data and return the results when the analysis is complete. Depending on the size of the dataset, the analysis may take a few minutes to 1+ hour.

Running MaAsLin 2 Workflow

Viewing the MaAsLin2 Results

MaAsLin3 (Microbiome Multivariable Association with Linear Models) is the latest iteration of the tool's framework, currently in beta testing.

MaAsLin3 for Differential Abundance

Running MaAsLin3 Workflow

Longitudinal and Complex Association Testing with MaAsLin3

Viewing the MaAsLin3 Results

The CHAMP™ Human Microbiome Profiler is a powerful taxonomic and functional pipeline that provides high-resolution insights into microbial communities. Utilizing advanced profiling methods, curated reference databases, and robust statistical models, CHAMP™ accurately identifies microbial species and integrates multi-omic data to reveal associations between microbiome diversity and health outcomes.

CHAMP™ Human Microbiome and Functional Profiling

KEPLER Host-Agnostic Taxonomic Profiling

Functional profiling from whole genome shotgun microbiome or metatranscriptomic short reads sequencing data provides crucial insights into the genomic potential of underlying molecular, biochemical and metabolic activities of microbial communities.

FUNCTIONAL Host-Agnostic Profiling

The Antimicrobial Resistance (AMR) and Virulence Factor (VF) profiling pipeline in CosmosID-HUB leverages KEPLER to provide high-resolution, accurate detection and quantification of resistance and virulence genes from sequencing data. This pipeline uses a sophisticated k-mer-based algorithm and the Resfinder database to achieve rapid and reliable analysis.

AMR/VF Profiling

16S Amplicon Classification

ITS Amplicon Classification

In metagenomics, biological specimens are sometimes collected from a tissue of a host that contains a high ratio of host to bacterial DNA. Removal of host DNA can increase precision and accuracy in microbiome profiling, especially for functional data.

Host Read Removal Workflow

Use the following links to download species lists for each database.

Database Species Lists

The bioinformatic pipelines within the CosmosID-HUB can be accessed via the Command Line through API integration.

These details are written for Terminal on Mac. Please adjust for Windows use.

Install and Setup

Running the CLI

Example: Running CHAMP

Update Log

Methods for Manuscripts

We have updated our Bacteria and Fungi databases.

Bacteria And Fungi Database Updates

CosmosID-HUB remains committed to maintaining the highest standards in security, compliance, and IT operations.

Security and IT Documentation

These datasets can be deposited into your account upon request for demo purposes

Available Example Datasets

The CosmosID-HUB utilizes GTDB-based nomenclature for taxonomic assessment.

GTDB vs. NCBI Taxonomic Nomenclature

An overview of how to get started with CosmosID

Create an Account

How to upload samples to CosmosID for analysis

Upload Samples

Import and analyze metagenomic samples from Illumina BaseSpace

BaseSpace Import

How to upload and analyze ZymoBIOMICS microbial community standards

Upload Microbiome Standard

Your CosmosID account contains your email address and other details, as well as the number of credits available in your account.

Your Account Details

NCBI SRA Import

Database Search

Unified Relative Abundance/Combined Kingdom Analysis

View Results

CosmosID provides a heat map for visualizing comparative analysis results.

Heat Map

3D PCA

Bioinformatics Concepts

Samples for metagenomic analysis are whole genome shotgun sequencing files - usually fastq or fasta files.

Metagenomic Classification

Amplicon Classification

16S Metagenomics - Taxonomy

Here are some definitions of terms we use in this guide.

Definitions

Methods

Users can query shotgun metagenomic samples against the Dark Matter Database (beta).

Dark Matter Database (Beta)

Good news! We have updated our Bacteria and Fungi databases.