Abstract 4956: A fast and efficient bioinformatics analysis workflow for processing reads from single-cell multiomics assays captured on a microwell-based platform

Abstract

Abstract Here, we present a significant update: version 2.0 of our sequencing analysis, it is a comprehensive primary analysis workflow that is up to 7X faster and consumes 2X less disk space than the previous release. We used it to process a library with 20,000 human PBMCs sequenced to a depth of 1.2 billion reads in 2.5 hours of wall-clock time. The pipeline can be used with reads from single-cell whole transcriptome, targeted mRNA, surface antigens (AbSeq), TCR/BCR and Sample Tag libraries captured on the BD Rhapsody™ System platform. The major processing steps include Quality Filtering, Cell Barcode Identification, Read Alignment, Feature Assignment, UMI Error Correction, Identification of Putative Cells, Sample De-Multiplexing, Dimensionality Reduction for Visualization and VDJ Contig Assembly and Annotation. Output files and metrics are available in easy-to-digest formats, including an html report with dynamic visualization. Integrated outputs in Seurat and Scanpy formats combine expression matrices and all cell annotation metadata (e.g., predicted cell type, sample assignment, TCR/BCR sequence and gene segments). These pre-generated files are ready to load into popular single-cell analysis tools. The pipeline uses CWL as the workflow manager and makes use of custom code written in C++ and Python along with various open-source packages for data processing. The pipeline can also process reads from non-human species and includes built-in support for specifying and building custom reference genome indices. In support of high-throughput multiomic discovery studies enabled by the BD Rhapsody™ HT Xpress System, this pipeline has been tested with datasets containing more than 800,000 putative cells and 14.5 billion reads. For Research Use Only. Not for use in diagnostic or therapeutic procedures. BD, the BD Logo and BD Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2023 BD. All rights reserved. NPM-2535 (v1.0) 1023 Citation Format: Raghavendra Padmanabhan, Brent Weichel, Amie Radenbaugh, Yuefu Jiang, Charles Weeks, Thomas McCarthy, Youngsook Kim, Anthony Berno, Devon Jensen. A fast and efficient bioinformatics analysis workflow for processing reads from single-cell multiomics assays captured on a microwell-based platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4956.