This pipeline processes single-cell RNA sequencing (scRNA-seq) data using the Piscem-Alevin-Fry workflow. It supports two execution modes:
- Serverless (AWS Lambda) — Parallel read mapping across multiple Lambda instances for large-scale speedup.
- On-server / Standalone (any Linux machine) — Reproduces the traditional on-server execution baseline from the paper, running the full pipeline locally with no cloud dependencies.
Both modes produce identical gene-by-cell count matrices.
The standalone script reproduces the "On-Server (SSD) Execution" baseline from the paper (Table 2). It runs the identical Piscem-Alevin-Fry pipeline on any Linux x86_64 machine:
git clone https://github.com/BioDepot/scRNA-serverless.git
cd scRNA-serverless
bash scripts/e2e_standalone_pbmc.sh pbmc1kEverything (tools, reference data, FASTQs) is downloaded automatically from public sources. The pre-built reference index is archived on Zenodo (DOI: 10.5281/zenodo.19375096). See the On-Server Pipeline Guide for details.
| Guide | Description |
|---|---|
| On-Server Pipeline Guide | Run the on-server pipeline on any Linux machine — no credentials needed, everything downloaded automatically |
| Serverless Pipeline Guide | Step-by-step instructions to run the serverless pipeline on your own AWS account (requires AWS, us-east-2 region) |
| Reproducibility Notes | Automatic fallbacks for AWS account limits, configuration reference, and local disk requirements |