This repository contains the CWL and YML files necessary to run the BD Genomics Rhapsody Analysis Pipeline locally.
To obtain the files, click on Downloads in the left navigation panel, and then Download repository.
For more details on how to use these files, see the BD Genomics Analysis Setup User Guide (Doc ID: 47383).
BD Rhapsody™ WTA Analysis Pipeline:
- 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
BD Rhapsody™ Targeted Analysis Pipeline and BD Rhapsody™ WTA Analysis Pipeline:
- 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
BD Rhapsody™ Targeted Analysis Pipeline and BD Rhapsody™ WTA Analysis Pipeline:
- Added Sample_Tag_ReadsPerCell.csv to Multiplex Output
- Optimized pipeline in various steps for memory usage
- Fixed bug in status determination for UMI_Adjusted_Stats.csv file
BD Rhapsody™ Targeted Analysis Pipeline:
- Updated Targets section in Metrics_Summary.csv to calculate metrics based on targets detected in putative cells only
- Removed Clustering Analysis and outputs
BD Rhapsody™ WTA Analysis Pipeline:
- Added support for BD™ AbSeq libraries
- Removed Targets section in Metrics_Summary.csv for WTA only libraries
- Removed Pct_Error_Reads and Error_Depth in UMI_Adjusted_Stats.csv, which are not applicable to WTA only libraries
- Added BD Rhapsody™ WTA Analysis Pipeline
- Fixed bug that can cause stalling when zero putative cells were identified
- Fixed bug that affected runs using Disable Refined Putative Cell Calling option
- Increased memory limits for GetDataTable and Metrics
- Fixed bug associated with "No Multiplex" option on SBG
- Uses fewer resources in AddToSam step.
- Added new options for putative cell determination:
- Exact Cell Count: Set a specific number of cells as putative, based on those with the highest error-corrected read count
- Disable Refined Putative Cell Calling: Determine putative cells using only the basic algorithm
- Updated to Python 3
- Updated alignment defaults (minor molecule count changes expected)
- Local install only - CWL files are bundled into one file
- Added support for BD Single-cell multiplexing kit – Mouse Immune
- Updated various filtering thresholds to support sequencing runs with shorter read length
- Deprecated pipeline input – BAM input
- Fixed bug in Quality Filter (minor metrics changes expected)
- Optimized pipeline (computationally faster, more scalable to support larger input data size, and better logging)
- Added support for BD™ AbSeq assay
- Added support for BD™ single-cell multiplexing kit - Mouse Immune
- New pipeline input - AbSeq Reference
- New pipeline outputs - Unfiltered cell-gene data tables
- Updated Metrics_Summary.csv to support metrics from multiple sequencing libraries
- Updated Recursive Substitution Error Correction (RSEC) algorithm (minor molecule count changes expected)
- Optimized pipeline to run faster
- Added support for BD Single-cell multiplexing kit - Human
- Improved pipeline speed by deleting large temp files
- Removed network requirement when running locally
- bug fix for the wrong docker image name - Dec 13, 2017