Getting Started
Welcome to the Pango.Network analysis platform. Our goal is to provide a powerful, accessible interface for SARS-CoV-2 genomic analysis. You can interact with our platform in three primary ways:
Web Interface
GUI
The easiest way to analyze sequences. Drag, drop, and get results.
Command Line
CLI
In-browser CLI for quick job management and status checks.
REST API
Programmatic
Integrate analysis into your automated pipelines.
Using the Graphical Interface
The GUI is the easiest way to get started with your analysis. Follow these steps:
Step 1
Navigate to the Analyze Page
Click the "Analyze" button in the header navigation.
Step 2
Upload Your Data
Drag and drop a sequence file onto the upload area, or click to browse your local files. The file should contain one or more SARS-CoV-2 genome sequences.
Supported formats: FASTA (.fasta, .fa, .fna), GenBank (.gb, .gbk), FASTQ (.fastq, .fq)
Compression: .gz and .zip files are automatically decompressed
Step 3
Select Tools
By default, both Pangolin and Nextclade are selected for analysis. In the future, you will be able to select or deselect specific tools.
Step 4
Start Analysis
Click the "Start Analysis" button. Your file will be uploaded, and the analysis job will be submitted.
Step 5
Monitor Progress
You will see real-time status updates as your job is processed. Once complete, a link to the results page will appear.
Using the Command Line
For users who prefer a command-line environment, our in-browser CLI provides direct access to job management.
Available Commands
helpDisplays a list of all available commands.
status <job-id>Checks the current status of a submitted analysis job.
results <job-id>Fetches and displays the results for a completed job.
clearClears the terminal screen.
Pro Tip
API Reference
Our REST API allows for programmatic submission and retrieval of analysis jobs. This is ideal for integration into automated bioinformatics pipelines.
Base URL
https://pango.network/api/v1Supported File Formats
Sequence Formats
.fasta, .fa, .fna
.gb, .gbk, .genbank
.fastq, .fq (with quality filtering)
Compression
.gz (auto-decompressed)
.zip (auto-extracted)
Endpoints
POST /analyze
Submit Analysis Job
Submits a new analysis job. The request must be a multipart/form-data request. Supports FASTA, GenBank, FASTQ formats and compressed files (.gz, .zip).
Parameters
fileSequence file (FASTA, GenBank, or FASTQ format).
toolsComma-separated tools. Default: "pangolin,nextclade,scorpio"
optionsJSON string with additional options (see below).
Options Object
analysis_mode"fast" | "accurate" | "comprehensive"
include_phylogeneticboolean - Include UShER tree placement
min_lengthnumber - Minimum sequence length
fastq_min_qualitynumber - Min quality score for FASTQ (default: 20)
Response
1{2 "job_id": "uuid-string",3 "status": "queued",4 "sequence_count": 10,5 "status_url": "/v1/jobs/{job_id}",6 "results_url": "/v1/results/{job_id}"7}Example cURL Request
1# Basic request2curl -X POST "https://pango.network/api/v1/analyze" \3 -F "file=@sequences.fasta"4 5# With options6curl -X POST "https://pango.network/api/v1/analyze" \7 -F "file=@sequences.fasta.gz" \8 -F "tools=pangolin,nextclade" \9 -F 'options={"analysis_mode":"fast","min_length":25000}'GET /jobs/{job_id}
Get Job Status
Retrieves the current status and progress of an analysis job.
Response
1{2 "job_id": "uuid-string",3 "status": "processing", // queued | processing | completed | failed | cancelled4 "progress": 45.5,5 "current_tool": "pangolin",6 "sequence_count": 100,7 "processed_count": 45,8 "created_at": "2024-01-15T10:30:00Z",9 "started_at": "2024-01-15T10:30:05Z",10 "completed_at": null,11 "error_message": null12}Example cURL Request
1curl "https://pango.network/api/v1/jobs/your-job-id-here"GET /jobs
List All Jobs
Retrieves a list of all submitted jobs, ordered by creation date (newest first).
Example cURL Request
1curl "https://pango.network/api/v1/jobs"GET /results/{job_id}
Retrieve Results
Retrieves the full analysis results for a completed job.
Response (Completed Job)
1{2 "summary": {3 "count": 10,4 "tools_used": ["pangolin", "nextclade", "usher"],5 "parallel_execution": true6 },7 "results": [8 {9 "sequence_name": "seq1",10 "pangolin": {11 "lineage": "XBB.1.5",12 "confidence": 0.9813 },14 "nextclade": {15 "clade": "23A",16 "qc.overallStatus": "good"17 }18 }19 ],20 "tree": "newick-tree-string"21}Example cURL Request
1curl "https://pango.network/api/v1/results/your-job-id-here"DELETE /jobs/{job_id}
Cancel Job
Cancels a queued or processing job. Completed or failed jobs cannot be cancelled.
Example cURL Request
1curl -X DELETE "https://pango.network/api/v1/jobs/your-job-id-here"POST /files/upload
Upload File
Upload a file to temporary storage and receive a handle for later use with the analyze endpoint.
Response
1{2 "filename": "sequences.fasta",3 "file_handle": "temp/uuid/sequences.fasta"4}Example cURL Request
1curl -X POST "https://pango.network/api/v1/files/upload" \2 -F "file=@sequences.fasta"Interactive API Documentation
Tool Guides
Pangolin
Lineage Assignment Tool
Pangolin (Phylogenetic Assignment of Named Global Outbreak LINeages) is the core tool for assigning Pango lineages. It takes a FASTA file of SARS-CoV-2 sequences and, using a machine learning model, assigns the most likely lineage to each sequence.
Interpreting Results
The assigned Pango lineage (e.g., B.1.1.7, XBB.1.5).
Level of conflict in phylogenetic placement. Lower is better.
Uncertainty score. Higher scores mean more uncertainty.
Nextclade
Sequence Analysis Tool
Nextclade is a powerful tool for in-depth sequence analysis. It performs clade assignment, mutation calling, and quality control checks.
Interpreting Results
The assigned Nextstrain clade (e.g., 21L, 22B).
Quality control assessment (good, mediocre, bad).
Number of nucleotide substitutions vs reference.