TABLE 2.

Tools for reads mapping and expression quantification of scRNA‐seq data.

Tools	Function	Language	URL
CellRanger	Analyse pipelines	Python	https://support.10xgenomics.com/single‐cell‐gene‐expression/software/pipelines/latest/what‐is‐cell‐ranger
DropEst	Analyse pipelines	C++	https://github.com/hms‐dbmi/dropEst
Kallisto–BUStools	Reads mapping	Python,R	https://www.kallistobus.tools/getting_started
Alevin	Reads mapping	Rust	https://salmon.readthedocs.io/en/latest/alevin.html
Cufflinks	Expression quantification	Python	https://github.com/cole‐trapnell‐lab/cufflinks
RSEM	Expression quantification	C++	https://github.com/deweylab/RSEM
Stringtie	Expression quantification	C++	https://github.com/gpertea/stringtie
SAVER	Expression quantification	R	https://github.com/mohuangx/SAVER