RNAquarium

RNAquarium is a Nextflow (DSL2) pipeline for reprocessing public RNAseq datasets at species scale. Starting from raw SRA runs, it filters host reads and produces gene counts and non-host reads (Part I), then assembles and taxonomically classifies the remaining non-host content (Part II).

RNAquarium enables:

• Retrieving and quality-filtering RNAseq runs directly from the SRA
• Filtering host reads by repeated alignment to a host genome — for zebrafish, retaining ~0.7% of input reads (~11 billion of 1.64 trillion across 77,188 runs) as "possible nonhost"
• Producing per-dataset gene counts tables
• Assembling and taxonomically classifying non-host reads, including viruses (Part II: metatranscriptomics)

Explore, visualize, and interact with RNAquarium project data — including via a chatbot — at the RNAquarium Portal.

Please refer to the documentation for full installation, parameters, and pipeline reference.

Part I — Transcriptomic + Filtering

• Inputs and Databases
• Non-host pipeline overview
• Getting Started (installation & usage)
• Parameters
• Pipeline Explanation
• Technical Notes

Part II — Metatranscriptomics

• Metatranscriptome pipeline overview (usage)
• Metatranscriptome Technical Notes
• Metatranscriptome virus-steps Technical Notes

For test-running RNAquarium on a SLURM cluster with a tiny, fully reproducible two-sample zebrafish example refer to the walkthrough.

RNAquarium is developed and maintained by the Computational Biology Platform & Balla Group at the Biohub.

• Research Lead Team: Keir Balla, Duo Peng, Yasin Şenbabaoğlu
• Bioinformatics Team: Yttria Aniseia, Eric Waltari, Max Frank, Gibraan Rahman, Andy Zhou, Yang-Joon Kim, Hejin Huang
• Web Development Team: Leandro Lima, Wellington Rutes

This project follows the Code of Conduct. By participating, you are expected to uphold it.

RNAquarium is released under the BSD 3-Clause License. Copyright (c) Biohub.