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.
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.
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User's Guide
For Research Use Only. Not for use in diagnostic or therapeutic procedures.