2.1.3

2.1.3

2024.10.9

• New Features: Added 5' single-cell RNA analysis and single-cell VDJ analysis modules.
• This update is released in a tar.gz compressed file format, allowing users to directly extract it without additional configuration of the computing environment.
• The conda installation method has been removed, and suspend updates for container method.
• A new feature for checking and correcting GTF file formats has been added.
• Fixed a memory issue that occurred during bead merging analysis in scATAC.
• Optimized the time consumption for RNA alignment and interval annotation.

2.1.2

2024.4.24

• Adjusted the algorithmic part of ATAC analysis: first, perform merging based on Jaccard index, then use peak region fragments for cell calling.
• Added multiple filtering parameters and the "bam" parameter to ATAC, enabling the generation of BAM format files.
• Added a chloroplast parameter to ATAC database mkref, removing mitochondrial and chloroplast transcription regions from the generated "tss.bed" file.
• Adjusted the webpage report for ATAC, maintaining consistent styling with RNA reports.
• Optimized the software installation steps, removing the R package section.
• In the RNA filtering section, changed the logic from filtering reads containing "N" to filtering out cell barcode and UMI regions containing "N".

2.1.1

2023.09.21

• Optimization：Adjusted the magnetic bead merging cell algorithm.
• Fix：Fixed the issue with marker gene display.
• Fix：Addressed excessive memory consumption in certain Docker versions.
• Fix：Resolved image output errors in the container version ATAC workflow report.

2.1.0

2.1.0

2023.7.28

• Add：single-cell ATAC analysis workflow.
• Optimization：single-cell RNA reference database construction.
  Updating to version 2.1.0 requires re-updating the reference database. Use the parameter '--noindex' to skip scSTAR index generation.
• Optimization：single-cell RNA analysis uses scanpy instead of seurat package to reduce analysis time.

2.0.7

2.0.7

2022.11.4

• Added：When filtering cDNA libraries with fastq, clipping filtering of adapters has been added.
• Added：Since the release of the new version of the reagent and the library structure are not suitable for judgment, in this version, we have added automatic judgment of the reagent version and dark reaction sequencing. Added parameters --chemistry, --darkreaction, used --customize to replace the previous --cDNAconfig and --oligoconfig, and removed the parameter --mixseq. It is recommended to automatically determine the reagent version and dark reaction sequencing. For parameter descriptions, please refer to the detailed description and FAQ question 1. Automatic judgment is currently only applicable to the DNBC4tools command line, not for wdl.
• Fix：Fixed several bugs and added the memory limit parameter --limitGenomeGenerateRAM in DNBC4tools mkref.
• Fix：Modified the software instructions.

2.0.6

2.0.6

2022.09.19

• Fix：Fixed an issue where results could not be reproduced, now we can make the results of multiple analyses exactly the same.
• Fix：Fixed bug in cDNA library reads Q30 statistics.
• Fix：Fix the problem that the number of barcodes in barcodes.tsv.gz is inconsistent with Estimated number of cells.
• Added：Added instructions for using singularity.
• It's recommended to upgrade this version, git clone the repo and then update the emvironment by pip install --upgrade dnbc4tools.

2.0.5

2.0.5

2022.08.19

• Update： Add docker version.
• Fix： There is a problem with the annotation logic statistics in 2.0.0, and 2.0.5 has been corrected.
• Fix： Fixed some description in html.
• Fix： The 2.0.0 was too strict with the format of gtf file, we change it.If there is no "gene_name" in the gtf file, "gene_id" is used by default, and if there is no "transcript_name", "transcript_id" is used by default.
• Fix： Adjusted umi correction.
• Fix： Fix the problem that the head of gtf need '#' when filtering gtf.
• It's recommended to upgrade this version, git clone the repo and then update the emvironment by pip install --upgrade dnbc4tools.

version2.0

version 2.0.0
2022.06.20

Update： The software is updated to version 2.0, which can use wdl and command line mode.
Fix： The process interruption caused by empty beads similarity analysis, and errors in QC and clustering when the number of cells is small.
Optimization： Reduce the time and memory used for alignment and annotation. Intronic reads are added by default in the annotation for expression analysis; the emptydrops method is added in the cell calling step, which is used by default; the display results of the pictures in the result report are optimized.
Added： Saturation analysis; annotation of cell clustering; added Fraction Reads in cells results.

version1.0

add some help documents