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.
Pipeline Overview
After sequencing, the pipeline takes input from FASTQ files, a reference (Targeted panel or WTA genome archive), an AbSeq reference (if required), and a supplemental reference (if required), using those to generate molecule counts per cell and metrics about the pipleline 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
v2.2.1 BD Rhapsody™ Sequence Analysis Pipeline
June 05, 2024
Additions
- Support for MGI sequencer FASTQ read header and file names
- For TCR/BCR assay, new output of a compressed bundle of PNG images showing the per chain VDJ DBEC algorithm thresholds
- Long read support - added new pipeline parameter for enabling support for long R2 reads (>650 bp) - default is to auto-detect long or short reads
Updates
- Ability to customize STAR and BWA-MEM2 alignment parameters, enabled on Seven Bridges and local runs
Fixes
- Failures that could occur with MGI sequencer FASTQ files in the QualCLAlign or AlignmentAnalysis nodes
- Failure caused by VDJ AssembleAndAnnotate node – Argument list too long
- Failure caused by MergeBam node – Argument list too long
- PhiX aligned reads could incorrectly be counted as targeted mRNA reads when using a targeted panel (usually these are already removed during FASTQ generation)
v2.2 BD Rhapsody™ Sequence Analysis Pipeline
April 19, 2024
Additions
- Added support for ATAC-Seq Assay and Multiomic ATAC-Seq Assay (WTA+ATAC-Seq)
- Added ability to customize STAR alignment parameters
Updates
- Updated the immune cell type classifier to be more lenient in the percentage of bioproducts required to run
- Updated TCR BCR annotation software IGBlast to version 1.22
- Updated TCR BCR annotation to IMGT release 202349-3 (12-06-2023)
- Updated bead version detection
Fixes
- Fixed error in dimensionality reduction when zero variable genes are found due to very sparse data
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
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User's Guide
