BD Rhapsody™ Analysis Pipeline Updates

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• v1.11 BD Rhapsody™ Targeted Analysis Pipeline and BD Rhapsody™ WTA Analysis Pipeline Released:

  • Added a pipeline report HTML that contains information about the analysis including the metrics summary and graphs to visualize the results
  • By default, reads aligned to exons and introns are now considered and represented in molecule counts. Added parameter to control this behavior.
  • Added new "Alignment Categories" for TCR and BCR reads
  • Added support for VDJ Adaptive Immune Receptor Repertoire (AIRR) standard format
  • For pipeline run where putative cells are determined based on AbSeq (protein) counts, added file output of cell IDs corresponding to suspected protein aggregates
  • Updated CWL workflow on Seven Bridges to fix memory failures and dynamically allocate resources for large datasets
  • Improved flexibility for FASTQ file naming
  • Updated Picard to version 2.27.4
  • Updated bead version detection
• v1.10.1 BD Rhapsody™ Targeted Analysis Pipeline and BD Rhapsody™ WTA Analysis Pipeline Released:
  • Fixed issue with cell label detection on reads from TCR/BCR, when TCR/BCR libraries were combined with other library types (WTA, Targeted, AbSeq) in a single sequencing index
  • Fixed issue with processing FASTQ files whose filenames end in “fq.gz”
• v1.10 BD Rhapsody™ Targeted Analysis Pipeline and BD Rhapsody™ WTA Analysis Pipeline Released:

  • Updated VDJ pipeline with support for full-length contig assembly, improved performance, new metrics, and new output files containing contig sequences

  • Added support for Rhapsody Enhanced Beads, with automatic bead version detection
  • Added option to call putative cells based on AbSeq read counts (for troubleshooting only)
  • Added “Alignment Categories” section to metric summary which provides a breakdown of the types of alignments seen for each library
  • Added separate metric summary files for each sample tag for experiments using BD Single-Cell Multiplexing kits
  • Renamed various metrics in outputs to reflect multi-omics nature of data (Target Type → Bioproduct_Type, Gene/Target → Bioproduct)
  • Added Pct_Read_Pair_Overlap and Median Reads Per cell metric to metric summary
  • Improved support for larger runs on SBG
  • Optimized pipeline metadata handling
  • Improved checking of reference files
• v1.9.1 of the BD Rhapsody™ Analysis Pipeline for improved WTA Analysis Released:
  • Improved putative cell calling algorithm to reduce overcalling of putative cells in high cell input experiments
  • Updated alignment settings to improve AbSeq mapping when R2 read length is greater than 75 bases
• v1.9 BD Rhapsody™ Targeted Analysis Pipeline and BD Rhapsody™ WTA Analysis Pipeline Released:
  • Improved FASTQ file pairing - filenames are flexible and pairing is now based on read sequence identifier
  • Optimized pipeline in various steps for memory and storage usage
  • Fixed bugs related to Sample Multiplexing Kit noise and DBEC mean molecule metric
  • BD Rhapsody™ Targeted Analysis Pipeline:
    • Support for BD Rhapsody™ VDJ CDR3 protocol
    • Read and molecule counts for targets from same gene symbol are combined in the output tables
    • Updated Bowtie2 alignment parameters for improved sensitivity
  • BD Rhapsody™ WTA Analysis Pipeline:
    • Updated Pct_Cellular Metrics calculations to match Bioinformatics handbook descriptions
    • Added support for supplemental reference fasta files, which allow alignment to transgenes, like viral RNA or GFP
    • Updated STAR alignment parameters for improved sensitivity