PT  - JOURNAL ARTICLE
AU  - Booeshaghi, A. Sina
AU  - Pachter, Lior
TI  - Benchmarking of lightweight-mapping based single-cell RNA-seq pre-processing
AID  - 10.1101/2021.01.25.428188
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.01.25.428188
4099  - http://biorxiv.org/content/early/2021/03/03/2021.01.25.428188.short
4100  - http://biorxiv.org/content/early/2021/03/03/2021.01.25.428188.full
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.