scafari: exploring scDNA-seq data

Abstract

Summary: Recent advances in single-cell sequencing made it possible to not just analyze a cell's individual expression pattern, but to gain insights into a single cell's genome using the cutting-edge technology single-cell DNA sequencing. Mission Bio is, with the Tapestri platform, one of the few providers of this technology. So far, however, there is only little open-source software available for user-friendly processing and quality analysis of this data type. With scafari, we present a tool that offers easy-to-use data quality control as well as explorative variant analyses and visualization.

Availability and implementation: scafari is implemented as an R Bioconductor package featuring a shiny application and is available at https://bioconductor.org/packages/scafari.

Figure 1.

Schematic overview of scafari’s analysis workflow and exemplary results. The analysis is divided into four steps, represented by corresponding tabs: (A) “Sequencing,” (B) “Panel,” (C) “Variants” and (D) “Explore Variants.” An exemplary excerpt from a scafari analysis of test data shows (E) the amplicon distribution over the genome, (F) the VAF heatmap with the variants of interest over all filtered cells annotated with genotype, (G) the PCA of k-means clustered cells, and (H) the VAF distribution, PCA with noted VAFs per cell and genotype abundance for every selected variant of interest.