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Spl-IsoQuant

This is a fork of the original IsoQuant project. The same group maintains both repositories equally.

Spl-IsoQuant is a tool for the genome-based analysis of long RNA reads, such as PacBio or Oxford Nanopores. Spl-IsoQuant can perform the following analysis:

  • Quantification:
  • Gene and transcript quantification;
  • Exon, splice junction, and intron retention quantification;
  • Detecting PolyA site and TSS;

  • Per-condition quantification (counts grouping);

  • Isoform and gene discovery:

  • Annotation-based isoform discovery;
  • De novo transcript and gene discovery;

  • Fusion gene discovery;

  • Single-cell and spatial transcriptomic analysis:

  • Barcode calling for 10x single-cell, 10x Visium and Visium HD, Curio, Stereo-seq;
  • Universal barcode calling for user-specified protocols;
  • PCR deduplication;
  • Per-barcode and per-cell-type quantification;

The latest Spl-IsoQuant version can be downloaded from https://github.com/algbio/spl-IsoQuant/releases/latest.

Spl-IsoQuant pipeline for single-cell and spatial transcriptomic data

Pipeline

Spl-IsoQuant pipeline for bulk data

Pipeline