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Welcome to the SQANTI3 Documentation!

Contents:

• Introduction to SQANTI3

• Dependencies and installation

• Version history

• Isoform classification: categories and subcategories

• Running SQANTI3 from the wrapper

• Running SQANTI3 quality control

• TUSCO quick start (SQANTI3 QC)

• TUSCO-novel (Novel Isoform Stress Test)

• Understanding the output of SQANTI3 QC

• IsoAnnotLite

• Running SQANTI3 filter

• Running SQANTI3 rescue

• Tutorial: running SQANTI3 on an example dataset

• Running SQANTI-reads

• Memory requirements to use parallelization