Release Notes

Official release history of DNBelab C Series™ HT Single-Cell Analysis Software

◆ Latest Release • ◆ All Versions • ◆ Version Guide

⚠️ Beta Notice: This version is feature-complete but may contain bugs. Community testing and feedback are welcome! For production environments, please use the latest stable release.

RNA-Seq Enhancements

Alignment & Annotation: Prioritized exonic loci for improved accuracy and better handling of multi-gene mapped reads.
Barcode Processing: Added correction for cell barcodes with ambiguous 'N' bases.
Dual-Species Support: Full support to build and analyze dual-species references.
Output Improvements: Enhanced BAM files (CC/CB tags), three-column feature matrix (ID, name, type), and updated web reports.
Parameter Updates: Auto-estimated `expectcells` and a new `minumi` parameter.

ATAC-Seq Enhancements

QC & Reporting: Added Q30 statistics for barcodes/reads and insert size distribution from deduplicated fragments.
Technical Updates: Upgraded chromap to v0.3.3, improved barcode correction, and enhanced BAM output.

VDJ Enhancements

Assembly & Annotation: Advanced per-cell assembly for full-length contigs and stricter filtering.
Performance: Removed full data preload requirement for low-memory analysis.
Output & Reporting: Enhanced `contig_annotations.csv`, improved QC metrics, and added consensus sequence annotations.
Compatibility: Custom reference support for non-human/mouse species.

Cross-Module Improvements

Standardized `customize` parameter across all modules.
Significant storage reduction through optimized file structure.
Removed intermediate files and `process` parameter functionality.

New Features

Added RNA 5' transcriptome analysis module
Added single-cell VDJ analysis module
GTF file format checking and correction functionality

Installation & Performance

Released as tar.gz with no additional environment configuration needed
Removed conda installation method
Fixed memory exceptions in scATAC bead merging
Optimized RNA alignment and interval annotation performance

ATAC Analysis Improvements

Updated algorithm: Jaccard-based merging → cell calling via peak fragments
Added multiple filtering parameters and BAM format support
Enhanced chloroplast handling in database construction
Unified web report style with RNA analysis

General Improvements

Streamlined installation process (removed R package requirements)
Improved N filtering logic for cell barcodes and UMI regions

RNA Workflow Optimization

Bead merging analysis using oligo data before cell calling
Enhanced marker gene display (top 50 genes by log2 fold change per population)

Bug Fixes

Fixed high memory usage in container versions
Resolved ATAC report image display issues

Major Addition

New ATAC analysis module

RNA Module Updates

Optimized reference database construction with `ref.json` information file
Replaced Seurat with Scanpy for faster dimensionality reduction and clustering

Automation & Parameters

Automatic recognition of reagent versions and sequencing dark cycles
New parameters: `chemistry`, `darkreaction`, `customize` (replacing `cDNAconfig`/`oligoconfig`)
Removed `mixseq` parameter

Technical Improvements

Added adapter sequence trimming for RNA cDNA libraries
Memory parameter `limitram` for database construction with automatic optimization

Container & Reliability

Added Singularity container support
Fixed reproducibility issues for consistent results
Corrected cDNA library Q30 statistics and barcode count consistency

Container & Format Support

Added Docker image version
Reduced GTF format requirements (flexible gene_name/transcript_name handling)
Improved UMI correction logic and HTML report descriptions

Major Release

Command-line interface support
Enhanced workflow stability and error handling
Optimized alignment and annotation performance
Default emptydrops cell identification method
Added saturation analysis and cell cluster annotation

⚠️ **Production Recommendation**: Use the latest stable release for production environments. Beta versions are for testing and development only.

Version	Key Features	Recommended Use Cases
2.1.3+	RNA 5' + VDJ analysis modules	VDJ analysis, 5' RNA workflows
2.1.0+	ATAC analysis support	ATAC-seq analysis
2.0.0+	Command-line interface	Standard 3' RNA analysis