HBM-CITEseq: a uniform CITE-seq processing pipeline for the HuBMAP Consortium

As part of the HuBMAP Consortium we have been developing methods for uniformly processing and indexing multiple single-cell datasets, which enable efficient integration of data from different platforms. HuBMAP computational pipelines have so far focused on unimodal data types such as single-cell/nucleus RNA sequencing and single nucleus ATAC-seq. Here we present HBM-CITEseq, a processing pipeline for Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) datasets, the first multimodal sequencing processing pipeline for the HuBMAP Consortium, with transcriptomic outputs from HBM-CITEseq matching those of the HuBMAP RNA-seq pipeline. HBM-CITEseq is a CWL workflow wrapping command-line tools encapsulated in Docker images. It is freely available on GitHub at https://github.com/hubmapconsortium/citeseq-pipeline.