ASAP 2020 update: An open, scalable and interactive web-based portal for (single-cell) omics analyses

Fabrice P.A. David, Maria Litovchenko, Bart Deplancke, Vincent Gardeux

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

Single-cell omics enables researchers to dissect biological systems at a resolution that was unthinkable just 10 years ago. However, this analytical revolution also triggered new demands in 'big data' management, forcing researchers to stay up to speed with increasingly complex analytical processes and rapidly evolving methods. To render these processes and approaches more accessible, we developed the webbased, collaborative portal ASAP (Automated Singlecell Analysis Portal). Our primary goal is thereby to democratize single-cell omics data analyses (scRNAseq and more recently scATAC-seq). By taking advantage of a Docker system to enhance reproducibility, and novel bioinformatics approaches that were recently developed for improving scalability, ASAP meets challenging requirements set by recent cell atlasing efforts such as the Human (HCA) and Fly (FCA) Cell Atlas Projects. Specifically, ASAP can now handle datasets containing millions of cells, integrating intuitive tools that allow researchers to collaborate on the same project synchronously. ASAP tools are versioned, and researchers can create unique access IDs for storing complete analyses that can be reproduced or completed by others. Finally, ASAP does not require any installation and provides a full and modular single-cell RNA-seq analysis pipeline. ASAP is freely available at https://asap.epfl.ch.

Original languageEnglish (US)
Pages (from-to)W403-W414
JournalNucleic acids research
Volume48
Issue numberW1
DOIs
StatePublished - 2021
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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