Introduction

IsoTV is Snakemake pipeline to analyze and visualize functional features of translated transcript isoforms. IsoTV incorporates various tools to predict protein domains, secondary structure, disordered regions, and post-translational modification sites. The visualization facilitates comparison of the set of transcript isoforms expressed across conditions and explored the functional consequences of isoform differences. IsoTV supports a range of transcriptome sequencing technologies, including short-reads, Oxford Nanopore (ONT) long-reads, Pacific Bio-sciences (PacBio) long-reads. It also supports other inputs, including single or multiple gene sequences.

There are three major components to this tool:

• Raw ONT Reads Processing - Assembling a de novo based transcriptome from raw ONT signals or basecalled ONT reads. Also, generates remapped files to the constructed transcriptome and quantifies individual isoform expression levels.
• Isoform Transcript Processing - Translating isoform transcripts from mRNA sequences to amino acid sequences.
• Translated Isoform Feature Analysis - Processing and visualizing functional features for each isoform.

This documentation provides a comprehensive overview of pipeline. Below describes the outline of the key topics discussed in the documentation:

• Tools summarizes the external tools used for this pipeline.
• Installation discusses hows to install the pipeline as well as all the prerequisite tools needed.
• Modules covers in depth of the various processes and tools within the pipeline.
• Tutorial describes about how to use the pipeline, as well snakemake basics and cluster computing capabilities.