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Pseudoalignment facilitates assignment of error-prone Ultima Genomics reads

Booeshaghi, A. Sina and Pachter, Lior (2022) Pseudoalignment facilitates assignment of error-prone Ultima Genomics reads. . (Unpublished)

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We analyze single-cell RNA-seq data sequenced with Ultima Genomics technology and find high error rates in and near homopolymers. To compensate for these errors, we explore the use of pseudoalignment for read assignment, and find that it can perform better than standard read alignment. Our pseudoalignment read assignment for Ultima Genomics data is available as part of the kallisto-bustools kb-python package available at

Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription Paper ItemCode Itemkb-python package
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 June 5, 2022; Version 2 - June 14, 2022. Methods: The code to reproduce all the figures and results in the preprint is available at and provides a complete description of the methods. Data Availability: All data used in this preprint is available on GEO under accession GSM5917802.
Record Number:CaltechAUTHORS:20220607-425123000
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Official Citation:Pseudoalignment facilitates assignment of error-prone Ultima Genomics reads. A. Sina Booeshaghi, Lior Pachter. bioRxiv 2022.06.04.494845; doi:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:115049
Deposited By: George Porter
Deposited On:08 Jun 2022 14:41
Last Modified:30 Jun 2022 17:51

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