Universal preprocessing of single-cell genomics data.
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ABSTRACT:
SUBMITTER: Booeshaghi AS
PROVIDER: S-EPMC10515959 | biostudies-literature | 2023 Sep
REPOSITORIES: biostudies-literature
Publications
Universal preprocessing of single-cell genomics data.
Booeshaghi A Sina AS Sullivan Delaney K DK Pachter Lior L
bioRxiv : the preprint server for biology 20230915
We describe a workflow for preprocessing a wide variety of single-cell genomics data types. The approach is based on parsing of machine-readable <i>seqspec</i> assay specifications to customize inputs for <i>kb-python</i>, which uses <i>kallisto</i> and <i>bustools</i> to catalog reads, error correct barcodes, and count reads. The universal preprocessing method is implemented in the Python package <i>cellatlas</i> that is available for download at: https://github.com/cellatlas/cellatlas/. ...[more]
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