Pigeon
Pigeon is a PacBio Transcript Toolkit that contains tools to classify and filter full-length transcript isoforms into categories against a reference annotation. Pigeon is based off of SQANTI3 and the output is compatible with downstream analysis with Seurat.
The pigeon tool is in beta. Expect continual changes, which may change the algorithm and or the command line interface.
Tools
| Tool | Description |
|---|---|
| sort | Transcript sorting |
| index | Annotation file indexing |
| classify | Transcript classification |
| filter | Transcript classification filtering |
| report | Transcript reporting |
| make-seurat | Generate Seurat-compatible matrices |
Input
- Collapsed isoforms in GFF format from IsoSeq collapse.
- Several reference input files required across all steps of the pigeon workflow are described here.
Execution
The CLI workflow is described here.
Availability
The latest version of pigeon is distributed through BioConda.
Versions
Version 1.0.0: Full changelog here