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Barcode, UMI, Set format and BUStools

Melsted, Páll and Ntranos, Vasilis and Pachter, Lior (2019) Barcode, UMI, Set format and BUStools. Bioinformatics, 35 (21). pp. 4472-4473. ISSN 1367-4803.

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We introduce the Barcode-UMI-Set format (BUS) for representing pseudoalignments of reads from single-cell RNA-seq experiments. The format can be used with all single-cell RNA-seq technologies, and we show that BUS files can be efficiently generated. BUStools is a suite of tools for working with BUS files and facilitates rapid quantification and analysis of single-cell RNA-seq data. The BUS format therefore makes possible the development of modular, technology-specific and robust workflows for single-cell RNA-seq analysis.

Item Type:Article
Related URLs:
URLURL TypeDescription Paper
Melsted, Páll0000-0002-8418-6724
Ntranos, Vasilis0000-0002-2477-0670
Pachter, Lior0000-0002-9164-6231
Additional Information:© 2019 The Author(s). Published by Oxford University Press. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model ( Received: 26 November 2018; Revision Received: 15 February 2019; Accepted: 11 April 2019; Published: 09 May 2019. We thank Fan Gao for helping with the benchmarking of 'kallisto bus' and BUStools. Valentine Svensson provided valuable suggestions, and we relied on his compilation of scRNA-seq read encodings (Svensson et al. 2017). Jase Gehring, Lynn Yi and Tina Wang provided valuable feedback on an initial kallisto-based scRNA-seq workflow, which motivated the development of the BUS format.
Issue or Number:21
Record Number:CaltechAUTHORS:20181128-093526289
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Official Citation:Páll Melsted, Vasilis Ntranos, Lior Pachter, The barcode, UMI, set format and BUStools, Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4472–4473,
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:91273
Deposited By: George Porter
Deposited On:28 Nov 2018 18:06
Last Modified:05 Nov 2019 15:50

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