TAMA (Transcriptome Annotation by Modular Algorithms) was designed for processing Iso-Seq data and other long read transcriptome data.
The main tools are described in the diagram below:
The TAMA package starts from a SAM/BAM file of reads mapped to a reference genome.
Please see the TAMA github wiki for details and instructions: https://github.com/GenomeRIK/tama/wiki
The code can be cloned and run without installation as long as you have access to Python 2.7.