Related Experiment Video
Updated: Dec 31, 2025
Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
Published on: March 12, 2021
Cloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco
Andrian Yang1,2, Abhinav Kishore1, Benjamin Phipps1
1Victor Chang Cardiac Research Institute, 405 Liverpool St, Darlinghurst, 2010, New South Wales, Australia.
Background:
Read alignment and transcript assembly are the core of RNA-seq analysis for transcript isoform discovery. Nonetheless, current tools are not designed to be scalable for analysis of full-length bulk or single cell RNA-seq (scRNA-seq) data. The previous version of our cloud-based tool Falco only focuses on RNA-seq read counting, but does not allow for more flexible steps such as alignment and read assembly.
Results:
The Falco framework can harness the parallel and distributed computing environment in modern cloud platforms to accelerate read alignment and transcript assembly of full-length bulk RNA-seq and scRNA-seq data. There are two new modes in Falco: alignment-only and transcript assembly. In the alignment-only mode, Falco can speed up the alignment process by 2.5-16.4x based on two public scRNA-seq datasets when compared to alignment on a highly optimised standalone computer. Furthermore, it also provides a 10x average speed-up compared to alignment using published cloud-enabled tool for read alignment, Rail-RNA. In the transcript assembly mode, Falco can speed up the transcript assembly process by 1.7-16.5x compared to performing transcript assembly on a highly optimised computer.
Conclusion:
Falco is a significantly updated open source big data processing framework that enables scalable and accelerated alignment and assembly of full-length scRNA-seq data on the cloud. The source code can be found at https://github.com/VCCRI/Falco.
