Release Notes

Author: SeekGene

Time: 2 min

Words: 265 words

Updated: 2026-10-13

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SeekArc™ Tools

v1.2.0

Added the seekarctools rna analysis module, providing an integrated workflow for RNA libraries from raw FASTQ files through expression matrix generation, cell identification, Seurat RDS generation, and GEX quality-control summaries. Optional paired-end alignment with STAR is also supported.
Added a stringent cell-identification mode for ARC multi-omics analysis to reduce the impact of low-quality barcodes on cell calling.

Replaced the fixed 20,000-cell limit for automatic cell identification with the configurable --max_cells parameter, and fixed the K-Means random seed to improve flexibility and reproducibility.
Optimized GTF parsing to reduce memory usage during Peak–Gene association analysis and improve compatibility with non-standard or complex GTF files.

Added the --chemistry parameter, supporting DD_AG, DD5_AG, and custom parsing configurations for RNA libraries. ATAC libraries use the DD_AA configuration.

Optimized the ATAC background threshold used for joint cell identification. Peak regions are extended by 2 kb upstream and downstream, overlapping intervals are merged, and background barcodes are filtered according to the fraction of the genome covered by the extended regions.
Set the maximum number of automatically identified cells to 20,000. When this limit is exceeded, candidate barcodes farther from the center of the background cluster are retained preferentially.
Changed the default Peak calling --qvalue from 0.05 to 0.001.

Released a stable version supporting the standard analysis workflow for SeekOne DD single-cell ATAC + RNA multi-omics data, including barcode extraction and correction, sequence alignment and quantification, joint cell identification, and generation of expression and Peak matrices.