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BD Rhapsody™ Sequence Analysis Pipeline

Overview

The BD Rhapsody^™Sequence Analysis Pipeline is a versatile tool that offers the flexibility to run your bioinformatics analysis on either a Seven Bridges cloud-based platform or on a local installation.

The BD Rhapsody^™Sequence Analysis Pipeline:

Provides a primary analysis of single-cell multiomics data by leveraging cutting-edge algorithms to deliver fast results and deep insights.
Utilizes an intuitive user interface via a cloud-based platform and is easy to use, regardless of the computational expertise of the user.
Offers the ability to choose between cloud-based or local installation options and affords maximum convenience and accessibility for single-cell multiomics data analysis.
Provides broad compatibility of output data with downstream analysis tools such as Seurat and Scanpy.

The .Cellismo output files from the BD Rhapsody^™ Sequence Analysis Pipeline can be imported into the BD Cellismo^™ Data Visualization Tool for secondary analysis and visualization.

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Pipeline Overview

After sequencing, the pipeline takes input from FASTQ files, a reference (Targeted panel or WTA / WTA+ATAC-Seq reference archive), an AbSeq reference (if required) and a supplemental reference (if required) to generate output files and metrics about the pipeline run.

Overview of the steps in the analysis pipeline.

Features

Free : Upload raw data, run the pipeline and download results from the cloud for free
Fast: Less than 3 hours to process 1 billion reads
Simple: One consolidated pipeline for BD Rhapsody^™ Whole Transcriptome Analysis Amplification Kit, BD Rhapsody^™ Targeted mRNA Kits, BD Rhapsody^™ TCR/BCR Next Multiomic Assays and BD Rhapsody^™ ATAC-Seq Assays

Release Notes

v2.3 BD Rhapsody™ Sequence Analysis Pipeline | March 2025

Additions

New .CELLISMO output file; for use in the BD Cellismo™ Data Visualization Tool. (Renamed and replaces the .H5MU output file)
Support for BAM file index for chromosomes longer than 500 Mb, with .bam.csi

Updates

ATAC index read minimum length changed from 43 to 35 bases
Renamed TCR/BCR metadata column from High_Quality_Cell to High_Qualty_Cell_TCR_BCR
Sample tag read start maximum position value to match prior pipeline versions
Make Rhapsody Reference tool to always include a 'gene_biotype' attribute
ATAC-Seq trimming of custom capture sequence improved to resolve edge cases in sequencing length
Improved logic for automatic paring of FASTQ filenames when header data is not formatted as expected
Seurat output file now includes additional metadata for sample tags and bioproduct stats

Fixes

Exact cell count parameter did not work for ATAC-Seq only or joint mRNA-ATAC cell calling
ATAC_Compile_Results node fails if custom Rhapsody reference did not have 'gene_biotype' GTF attribute
VDJ_Compile_Results node fails when there are zero cells detected
Custom Rhapsody Reference files for ATAC-Seq may fail if name ends with characters 'a' or 'n'
ATAC-Seq pipeline failure on certain AMD EPYC processors due to BWA-mem2 binary selection
ATAC-Seq pipeline failure in edge case where joint cell calling has no cell intersection
Pipeline report for ATAC-Seq run may report the wrong number of putative cells called
Pipeline failure caused by JSON parse on certain OS locales
Generate_Seurat node fails if there is only one AbSeq reference input
Failure in ATAC-Only pipeline run with sample tag when cell calling data has not been set
Extra Utility AnnotateCellLabelUMI fails if Run_Name parameter not provided

Get Free Access to the Pipeline

Cloud-Based Version

Go to Velsera.com
Click Request Access. In the request access window, enter your email address to receive an email invitation to the Seven Bridges Genomics platform within 24 hours.
Click the link in the email invitation and complete the registration. Seven Bridges Genomics displays the dashboard with the demo projects.

Local Version

Go to bitbucket.org/CRSwDev/cwl. If necessary, create a Bitbucket account.
In the left pane, click Downloads > Download Repository. The CWL and YML files will download.
Unzip the archive. Each folder within the archive is named after the pipeline version to which it corresponds.

Resources

User's Guide

BD Rhapsody™ Sequence Analysis Pipeline User's Guide

For Research Use Only. Not for use in diagnostic or therapeutic procedures.