Release Notes

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

◆ Latest Release • ◆ All Versions • ◆ Version Guide

RNA-Seq Enhancements

Alignment & Annotation: Refined prioritization of exonic loci to improve quantification accuracy and resolve multi-gene mapping ambiguities.
Barcode Processing: Implemented error correction logic for cell barcodes containing ambiguous 'N' bases.
Dual-Species Support: Added robust support for building and analyzing mixed-species reference genomes.
Output Improvements: Enriched BAM files with cell tags (CC/CB), updated feature matrices to include gene ID, gene name, and library type.
Parameter Updates: Introduced automatic estimation for expectcells and added a new minumi threshold parameter.

ATAC-Seq Enhancements

QC & Reporting: Expanded QC metrics to include barcode/read Q30 statistics and insert size distributions derived from deduplicated fragments.
Technical Updates: Upgraded alignment engine to chromap v0.3.3, enhanced barcode correction algorithms, and enriched BAM outputs.

VDJ Enhancements

Assembly & Annotation: Advanced per-cell assembly algorithms to maximize full-length contig recovery with stricter filtering criteria.
Performance: Optimized memory management to eliminate the need for full data preloading during analysis.
Output & Reporting: Enhanced contig_annotations.csv with comprehensive details, improved QC metrics, and added consensus sequence annotations.
Compatibility: Enabled support for custom reference generation for non-human/mouse species.

Cross-Module Improvements

Parameter Standardization: Unified the customize parameter usage across all analysis modules.
Storage Efficiency: Achieved significant reduction in disk usage through optimized file organization.
Workflow Optimization: Deprecated the process parameter and automated the cleanup of intermediate files to streamline execution.

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

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

Release Guidance:
Stable: Recommended for production environments; receives security and critical bug fixes.
Release Candidate (RC): Feature-complete builds intended for final validation and staging/pre-production. Minor bug fixes may still be applied. Not recommended for mission-critical production unless a version freeze is acceptable.
Beta: For testing and development only; APIs and behavior may change.