I am developing a web-based genomic-analysis workflow intended to make it easier for research teams to move from sequencing reads to reviewable variant outputs without managing every pipeline step manually.

The current workflow is designed around:

• FASTQ input for sequencing runs
• Configurable analysis workflow execution
• Variant calling output
• Variant annotation and filtering
• Variant review in a browser-based interface
• Traceable run/output records
• Exportable results for downstream analysis and reporting

The intended users are research laboratories, clinical genomics research teams, and translational genomics groups that want a more structured workflow around analysis outputs.

I am sharing it here to request technical feedback from people who regularly work with WGS, WES, FASTQ/BAM/VCF files, variant annotation, or genome-browser review.

The questions I would especially value feedback on are:

1. Which input formats and pipeline outputs are essential for your workflow?
2. What information must be visible before you trust a variant annotation or filtering result?
3. Which existing tools do you use for pipeline orchestration, annotation, and review?
4. What would make a browser-based workflow useful rather than a limitation?
5. What reproducibility information should be captured for every run (reference build, tool versions, parameters, QC metrics, provenance, etc.)?
6. Which export formats are non-negotiable for your lab?

ATGCFLOW is intended for research workflow support. It is not presented as a replacement for validated clinical diagnostic pipelines, expert variant interpretation, or institutional laboratory quality systems.

Project link: https://atgcflow.com

I would appreciate critical feedback, including reasons you would not use a tool like this. I am particularly interested in what is missing for real genomics workflows.