Universal preprocessing of single-cell genomics data

We describe a workflow for preprocessing a wide variety of single-cell genomics data types. The approach is based on parsing of machine-readable seqspec assay specifications to customize inputs for kb-python, which uses kallisto and bustools to catalog reads, error correct barcodes, and count reads....

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Detalles Bibliográficos
Autores principales: Booeshaghi, A. Sina, Sullivan, Delaney K., Pachter, Lior
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10515959/
https://www.ncbi.nlm.nih.gov/pubmed/37745572
http://dx.doi.org/10.1101/2023.09.14.543267
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author Booeshaghi, A. Sina
Sullivan, Delaney K.
Pachter, Lior
author_facet Booeshaghi, A. Sina
Sullivan, Delaney K.
Pachter, Lior
author_sort Booeshaghi, A. Sina
collection PubMed
description We describe a workflow for preprocessing a wide variety of single-cell genomics data types. The approach is based on parsing of machine-readable seqspec assay specifications to customize inputs for kb-python, which uses kallisto and bustools to catalog reads, error correct barcodes, and count reads. The universal preprocessing method is implemented in the Python package cellatlas that is available for download at: https://github.com/cellatlas/cellatlas/.
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spelling pubmed-105159592023-09-23 Universal preprocessing of single-cell genomics data Booeshaghi, A. Sina Sullivan, Delaney K. Pachter, Lior bioRxiv Article We describe a workflow for preprocessing a wide variety of single-cell genomics data types. The approach is based on parsing of machine-readable seqspec assay specifications to customize inputs for kb-python, which uses kallisto and bustools to catalog reads, error correct barcodes, and count reads. The universal preprocessing method is implemented in the Python package cellatlas that is available for download at: https://github.com/cellatlas/cellatlas/. Cold Spring Harbor Laboratory 2023-09-15 /pmc/articles/PMC10515959/ /pubmed/37745572 http://dx.doi.org/10.1101/2023.09.14.543267 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Booeshaghi, A. Sina
Sullivan, Delaney K.
Pachter, Lior
Universal preprocessing of single-cell genomics data
title Universal preprocessing of single-cell genomics data
title_full Universal preprocessing of single-cell genomics data
title_fullStr Universal preprocessing of single-cell genomics data
title_full_unstemmed Universal preprocessing of single-cell genomics data
title_short Universal preprocessing of single-cell genomics data
title_sort universal preprocessing of single-cell genomics data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10515959/
https://www.ncbi.nlm.nih.gov/pubmed/37745572
http://dx.doi.org/10.1101/2023.09.14.543267
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