DigestiFlow – Reproducible Demultiplexing for the Single Cell Era

We are happy to report that we have released our new software “DigestiFlow – Reproducible Demultiplexing for the Single Cell Era”

It is available under a permissive open source license via, contributions are welcome.


An ever-increasing number of NGS library preparation protocols used in biomedical research requires complex barcoding schemes. In combination with the economic urge to use deep multiplexing on high volume sequencing devices this has turned the once mundane task of demultiplexing into a complex and error prone analysis step. At the same time, many organizations do not have sophisticated computer-aided tools setup for assisting with this task. In this manuscript, we describe the package Digestiflow that focuses on the curation and management of Illumina flow cell raw data, in particular featuring excellent support for complex flow cell layouts. Namely, it allows for automated incorporation of flow cell runs, management of sample sheets, and the demultiplexing of Illumina base calls data. Digestiflow is an easy to implement, flexible, and extendable open source solution to address current and upcoming challenges in demultiplexing.

Further details can be found in the preprint

Last modified: Nov 17, 2020