Single Cell Genomics Tools

Tools used to analyse single-cell genomic data

Quality Control

PaSD-qc Evaluates the amplification properties and quality of single cell whole-genome sequencing data. Paper

Variant Calling

Monovar is a single nucleotide variant (SNV) detection and genotyping algorithm for single-cell DNA sequencing data. Paper

SCcaller identifies single nucleotide variations (SNVs) and short insertions and deletions (INDELs) from single cell sequencing data. Paper

Copy Number Variation

Ginkgo is a cloud-based single-cell copy-number variation analysis tool. Paper

Clonal Evolution

E-scape:

MapScape is a visualization tool for spatial clonal evolution.

TimeScape is a visualization tool for temporal clonal evolution.

Phylogeny

E-scape:

CellScape is a visualization tool for integrating single cell phylogeny with genomic content to clearly display evolutionary progression and tumour heterogeneity.

SiFit is a tool for reconstructing phylogenetic tree from noisy mutation profile of single cells. Paper