Comparative analysis of common alignment tools for single-cell RNA sequencing.

ABSTRACT:

Background

With the rise of single-cell RNA sequencing new bioinformatic tools have been developed to handle specific demands, such as quantifying unique molecular identifiers and correcting cell barcodes. Here, we benchmarked several datasets with the most common alignment tools for single-cell RNA sequencing data. We evaluated differences in the whitelisting, gene quantification, overall performance, and potential variations in clustering or detection of differentially expressed genes. We compared the tools Cell Ranger version 6, STARsolo, Kallisto, Alevin, and Alevin-fry on 3 published datasets for human and mouse, sequenced with different versions of the 10X sequencing protocol.

Results

Striking differences were observed in the overall runtime of the mappers. Besides tha

SUBMITTER: Bruning RS 

PROVIDER: S-EPMC8848315 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature