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

Booeshaghi, A. Sina and Pachter, Lior (2021) Benchmarking of lightweight-mapping based single-cell RNA-seq pre-processing. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20210126-131831766

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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.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2021.01.25.428188DOIDiscussion Paper
https://github.com/COMBINE-lab/BP_2021-lflRelated ItemCode
https://github.com/pachterlab/BP_2021Related ItemCode
ORCID:
AuthorORCID
Booeshaghi, A. Sina0000-0002-6442-4502
Pachter, Lior0000-0002-9164-6231
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.
Funders:
Funding AgencyGrant Number
NIHU19MH114830
Chan Zuckerberg InstituteUNSPECIFIED
Record Number:CaltechAUTHORS:20210126-131831766
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210126-131831766
Official Citation: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
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:107729
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:26 Jan 2021 21:41
Last Modified:04 Mar 2021 22:58

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