Single Cell Sequencing Quality Assessment: SCQUA

SCQUA is a program to help assessing the sequencing quality of single-cell data. It measures the sensitivity (detection limit) and the accuracy (correlation) according to the spike-ins (reference RNA).

It has performed analysis for a couple of single-cell sequencing benchmarking papers:

Comparative analysis of sequencing technologies for single-cell transcriptomics, KN Natarajan, Z Miao, et al. Genome Biology volume 20, Article number: 70 (2019)

High-throughput Full-Length Single-Cell RNA-Seq Automation L Mamanova, Z Miao, et al. (2020)

All the codes processing these data and making the figures are available in the example folder.

installation

To install the program please use the codes below:

git clone https://github.com/chichaumiau/SCQUA.git
cd SCQUA
python setup.py install

usage

Please refer to the examples for details about how to use the program.

Reference

Reference to the paper originated the measurement of scRNA-seq sensitivity and accuracy:

Power analysis of single-cell RNA-sequencing experiments V Svensson, KN Natarajan, et al. Nature Methods volume 14, pages381–387(2017)