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URL: https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/optimus
Proper Citation: Optimus Pipeline (RRID:SCR_018908)
Description: Optimus is a pipeline developed by the Data Coordination Platform (DCP) of the Human Cell Atlas (HCA) Project that supports processing of any 3' single-cell and single-nuclei expression data generated with the 10x Genomic v2 or v3 assay. It is an alignment and transcriptome quantification pipeline that corrects cell barcodes, aligns reads to the genome, corrects Unique Molecular Identifiers (UMIs), generates an expression matrix in a UMI-aware manner, calculates summary metrics for genes and cells, detects empty droplets, returns read outputs in BAM format, and returns gene counts in NumPy matrix and Loom matrix formats.
Synonyms: Optimus
Resource Type: data processing software, data analysis software, software resource, software application
Keywords: Data, single cell data, 10x technology data, cell bar code correction pipeline, reads alignment, genome, unique molecular identifier correction, mouse data sets analysis, human data sets analysis,
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