SpliceGrapher

MAJIQ, r MATS, MISO are widely used.

Splice-AI has been recently developed by Illumina for identification of splice variants affected by point mutations.

"Best" is highly subjective. It's all about the False Discovery Rate after you validate the differential splice predictions by RT-PCR and qPCR.

I didn't hear or use those proposed by others. My recommendation would be:

- CuffDiff

- SGSeq (R package going straight from sam/bam files)

- IsoformSwitchAnalyzeR (R package that parces parses cufflinks/cuffdiff output and others).

All of those have reasonably well written vignettes or manuals.

Utkarsh Kapoor Thank you for mentioning Splice-AI.

There's a lot of good info about alternative splicing analysis in this post: https://www.biostars.org/p/65617/

DiffSplice is another interesting one that I don't think has been mentioned.

Cameron J Grisdale Thanks for sharing the link.