Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS-Reference-Cited by-同舟云学术

Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS

Published:2019-08 Issue:4 Volume:2 Page:e201900371
ISSN:2575-1077
Container-title:Life Science Alliance
language:en
Short-container-title:Life Sci. Alliance

Author:

Afik Shaked¹^ORCID,Raulet Gabriel²,Yosef Nir¹³⁴⁵^ORCID

Affiliation:

1. Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA

2. Department of Computer Science, University of California, Davis, Davis, CA, USA

3. Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA, USA

4. Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA

5. Chan Zuckerberg Biohub, San Francisco, CA, USA

Abstract

RNA sequencing of single B cells provides simultaneous measurements of the cell state and its antigen specificity as determined by the B-cell receptor (BCR). However, to uncover the latter, further reconstruction of the BCR sequence is needed. We present BRAPeS (“BCR Reconstruction Algorithm for Paired-end Single cells” ), an algorithm for reconstructing BCRs from short-read paired-end single-cell RNA sequencing. BRAPeS is accurate and achieves a high success rate even at very short (25 bp) read length, which can decrease the cost and increase the number of cells that can be analyzed compared with long reads. BRAPeS is publicly available at the following link: https://github.com/YosefLab/BRAPeS.

Publisher

Life Science Alliance, LLC

Subject

Health, Toxicology and Mutagenesis,Plant Science,Biochemistry, Genetics and Molecular Biology (miscellaneous),Ecology

Reference23 articles.

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