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Benchmarking of lightweight-mapping based single-cell RNA-seq pre-processing

By A. Sina Booeshaghi, Lior Pachter

Posted 26 Jan 2021
bioRxiv DOI: 10.1101/2021.01.25.428188

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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