TY  - JOUR
A1  - Schulze Brüning, Ralf
A1  - Tombor, Lukas
A1  - Schulz, Marcel Holger
A1  - Dimmeler, Stefanie
A1  - John, David
T1  - Comparative analysis of common alignment tools for single-cell RNA sequencing
T2  - GigaScience
N2  - 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 that, Kallisto and Alevin showed variances in the number of valid cells and detected genes per cell. Kallisto reported the highest number of cells; however, we observed an overrepresentation of cells with low gene content and unknown cell type. Conversely, Alevin rarely reported such low-content cells. Further variations were detected in the set of expressed genes. While STARsolo, Cell Ranger 6, Alevin-fry, and Alevin produced similar gene sets, Kallisto detected additional genes from the Vmn and Olfr gene family, which are likely mapping artefacts. We also observed differences in the mitochondrial content of the resulting cells when comparing a prefiltered annotation set to the full annotation set that includes pseudogenes and other biotypes.
Conclusion: Overall, this study provides a detailed comparison of common single-cell RNA sequencing mappers and shows their specific properties on 10X Genomics data.
KW  - benchmarking
KW  - single-cell RNA sequencing
KW  - mapping-algorithms
KW  - aligners
KW  - transcriptomics
KW  - mappers
Y1  - 2022
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/63309
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-633097
SN  - 2047-217X
N1  - This study is supported by the Dr. Robert Schwiete Foundation, the Cardio-Pulmonary Institute Frankfurt, and the German Center for Cardiovascular Research (DZHK).
VL  - 11
IS  - 1
SP  - 1
EP  - 12
PB  - Oxford University Press
CY  - Oxford
ER  -