| Functions | Applications | Input files | Main output files | Programs | References |
| Characterize Nucleic-acid Feature | Explore the similarity between assembled and annotated transcripts in terms of the distribution of transcript length, exon length, G+C content | Confident transcripts; Reference transcripts | Diagnostic plots (barplot/density) | In-house scripts | Our study |
| Characterize Amino-acid Feature | Explore the similarity between assembled and annotated transcripts in terms of the distribution of amino acid-based features used in SAT | Confident transcripts; Reference transcripts | Diagnostic plots (barplot/density) | In-house scripts | Our study |
| Detect Alternative Splicing Events | Detect alternative splicing events in assembled transcripts | Alignment results (BAM); All transcript annotation file (GTF) | Alternative splicing events; Number of support reads | SGSeq (version 3.8; https://www.bioconductor.org/packages/release/bioc/html/SGSeq.html) | Goldstein et al., 2016 |