Spl-IsoQuant 2.4.0

• Improved recall for 10x single-cell barcode calling;

• Added cDNA splitting mode for 10x barcode calling;

• Improved exon and splice junction counts output (TSV matrix and mtx format);

• Added no_auto read grouping mode to avoid automatic grouping.

Spl-IsoQuant 2.3.0

• TSV output files do not have a # in headers for easier downstream processing (thanks to @yinshiyi).

• Fix Python 3.14 compatibility.

• Add --barcoded_bam flag for reading barcodes and UMIs directly from a input BAM.

• Add --barcode2barcode option for Visium HD data processing.

• Dramatic speed-up for 10x and universal barcode calling on large whitelists.

• Per-barcode counts grouping is now performed automatically if the barcodes are set.

Spl-IsoQuant 2.2.1

• Fix Python 3.8

• Fix MTX conversion.

• Fix --test message.

Spl-IsoQuant 2.2

• Support for 10x single-cell v3 and 10x Visium 3' data.

• Universal barcode detection via user-defined molecule structure.

• --read_group now supports multiple read grouping strategies. You can now simultaneously group counts by samples, BAM tags, barcode and barcode attributes, read attributes provided in separate TSV files or within read ids themselves.

• New --large_output option to control which large output files are generated.

• New --barcode2spot option that allows to group counts by barcode attributes, such as cell type or spatial location.

• Major performance improvements, especially related to Stereo-seq barocode detection.

Spl-IsoQuant 2.1

• Support for 10x Visium HD and Visium 3' data.
• Significant performance and usability improvements.

Spl-IsoQuant 1.0b

Repeat Spl-IsoQuant 1.0 to get Zenodo doi

Spl-IsoQuant 2.0

Spl-IsoQuant-2 for long reads obtained with Stereo-seq protocol.

Spl-IsoQuant 1.0

Spl-IsoQuant release 1.0, support Curio data analysis