TraceQC: An R package for quality control of CRISPR lineage tracing data

Abstract

MotivationThe CRISPR-based lineage tracing system is emerging as a powerful new sequencing tool to track cell lineages by marking cells with irreversible genetic mutations. Accurate reconstruction of cell lineages from CRISPR-based data is sensitive to noise. Quality control is critical for filtering out low-quality data points. Yet, existing quality control tools for RNA-seq and DNA-seq do not measure features specific for the CRISPR-linear tracing system. ResultsWe introduce TraceQC, a quality control package to overcome challenges with measuring the quality of CRISPR-based lineage tracing data and help in interpreting and constructing lineage trees. AvailabilityThe R package is available at https://github.com/LiuzLab/TraceQC. Contactzhandong.liu@bcm.edu or hyun-hwan.jeong@bcm.edu