| Input | Tool | Description |
| Transcript GFF | sort | Collapsed transcript GFF from isoseq collapse |
| Reference Annotation | index | Reference annotation in GTF format |
| Reference Genome | classify | Reference genome in FASTA format |
| FL Counts (Optional) | classify | FL count info from isoseq collapse (*.abundance.txt) |
| CAGE Peaks (Optional) | classify | CAGE peaks in BED format |
| polyA motif list (Optional) | classify | polyA motif list in custom format |
| Intropolis data (Optional) | classify | Intropolis data in custom format |
| Molecules FASTA | make-seurat | Molecules FASTA file from isoseq dedup |
| Groups txt file | make-seurat | Groups text file from isoseq collapse |