DOCUMENTATION

Run the current prototype locally.

This quickstart reflects the working local Flask prototype. A public pip install package and CLI repository are not yet published here.

01 / REQUIREMENTS

Before you begin

Python 3
A copy of kmeggie-prototype.zip supplied for evaluation
A local machine with enough space for the FASTQ files you intend to inspect

The current package is shared directly with evaluators; there is no verified public download link on this site.

02 / LOCAL QUICKSTART

Install and start the prototype

$ create an isolated Python environmentunzip kmeggie-prototype.zip
cd kmeggie-prototype
python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt
python app.py

When the local server starts, open http://127.0.0.1:5000 in the same machine’s browser.

Current architecture note

The local Flask QC engine and the CLI validators are prototype components. Their complete unified workflow is still in development.

03 / NO-INSTALL DEMO

Use the website prototype

Open the QC workspace.
Choose raw FASTQ or FastQC ZIP import. For raw FASTQ, select a QC guide and adjust its pass and review cutoffs if needed.
Run the 500-read synthetic sample or choose a supported local FASTQ file.
Review the checks, applied cutoffs, metrics, and charts. Changes to cutoffs take effect on the next run.
Export the report as HTML or JSON. Use Open JSON to reopen a saved report.

Open the live QC demo

04 / SUPPORTED INPUT

Prototype limits

Files	`.fastq`, `.fq`, and gzip-compressed variants
Records	Four-line, single-end FASTQ
Quality encoding	Phred+33
Local file size	50 MB
Decompressed size	100 MB
Read count	200,000 reads
Read length	100,000 bases per read

Files above a limit are rejected rather than sampled. Adapter detection, paired-end validation, and classification are not included.

05 / RELEASE STATUS

What is published

PUBLICBrowser QC demoOpen →

DIRECT ACCESSLocal prototype packageShared with evaluators

PENDINGPublic CLI packageNo pip install kmeggie claim yet

PENDINGPublic CLI source repositoryLink will appear after publication