For detailed information on the modules:

Input preparation: How to prepare the input alignment files.

Reconstructions: Given an alignment file and an assembled genome, this module will perform transcriptome reconstructions.

Quantifications Given a set of transcripts and sample aligned files, this module provides normalized read counts for each transcript in each sample as a matrix that is read to use in standard count-based differentially expression methods such as DESeq. For specific details on the input, output and how to run, please refer to the quantification manual

Link to paper

Link to paper: Link to paper