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

Creators: Booeshaghi, A. Sina; Pachter, Lior

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.

Additional Information

The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. Version 1 - January 26, 2021; Version 2 - March 3, 2021 We thank Diane Trout for sharing benchmarks that motivated this project. A.S.B. and L.P. were supported in part by NIH U19MH114830. The kallisto and bustools projects are supported in part by a grant for open source software from the Chan Zuckerberg Institute. We thank Mohsen Zakeri for suggesting in https://github.com/COMBINE-lab/BP_2021-lfl additions to the code-base to improve the reproducibility of the results in this manuscript. The code to download the data, perform the analyses and obtain the results is located at https://github.com/pachterlab/BP_2021 and provides a complete description of the methods. The authors have declared no competing interest.

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Submitted - 2021.01.25.428188v2.full.pdf

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