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

View ORCID ProfileA. Sina Booeshaghi, View ORCID ProfileLior Pachter
doi: https://doi.org/10.1101/2021.01.25.428188
A. Sina Booeshaghi
1Department of Mechanical Engineering, California Institute of Technology
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Lior Pachter
2Division of Biology and Biological Engineering and Department of Computing and Mathematical Sciences, California Institute of Technology
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  • For correspondence: lpachter@caltech.edu
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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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Improved reproducibility and added a mention to an additional tool.

  • https://github.com/pachterlab/BP_2021

Copyright 
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.
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Posted March 03, 2021.
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Benchmarking of lightweight-mapping based single-cell RNA-seq pre-processing
A. Sina Booeshaghi, Lior Pachter
bioRxiv 2021.01.25.428188; doi: https://doi.org/10.1101/2021.01.25.428188
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Benchmarking of lightweight-mapping based single-cell RNA-seq pre-processing
A. Sina Booeshaghi, Lior Pachter
bioRxiv 2021.01.25.428188; doi: https://doi.org/10.1101/2021.01.25.428188

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