Benchmarking of lightweight-mapping based single-cell RNA-seq pre-processing
AS Booeshaghi, L Pachter - bioRxiv, 2021 - biorxiv.org
bioRxiv, 2021•biorxiv.org
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.
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.
Abstract
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.
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