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Overview

The BD RhapsodySequence 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 RhapsodySequence 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.

 

 

 

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      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.

       

      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.