RT Journal Article
SR Electronic
T1 Benchmarking of lightweight-mapping based single-cell RNA-seq pre-processing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.01.25.428188
DO 10.1101/2021.01.25.428188
A1 Booeshaghi, A. Sina
A1 Pachter, Lior
YR 2021
UL http://biorxiv.org/content/early/2021/03/03/2021.01.25.428188.abstract
AB We compare and benchmark the two lightweight-mapping tools that have been developed for pre-processing single-cell RNA-seq data, namely the kallisto-bustools and Salmon-Alevin-fry programs. We find that they output similar results, and to the extent that there are differences, they are irrelevant for downstream analysis. However, the Salmon-Alevin-fry program is significantly slower and requires much more memory to run, making it much more expensive to process large datasets limiting its use to larger servers.Competing Interest StatementThe authors have declared no competing interest.