v1.3

Includes modules for quantification and differential isoform usage between conditions with replicates. Other speed improvements, bug fixes, and helper scripts for a smoother user experience.

v1.2

Enforces mapq>0 for supporting reads, correctSplice.py now replaced with ssCorrect.py. Other minor improvements/speed fixes

native RNA release

Includes options specific to isoform definition for nanopore native RNA sequencing reads i.e. using promoter regions to determine full-length isoforms and using aligned strand for a stranded protocol like native RNA sequencing. As seen in Workman et al. 2018 bioRXiv paper Nanopore native RNA sequencing of a human poly(A) transcriptome.

CLL release

FLAIR pipeline as used in Tang 2018 BioRXiv paper 'Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns'.