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.
|index||Annotation file indexing|
|filter||Transcript classification filtering|
|make-seurat||Generate Seurat-compatible matrices|
- Collapsed isoforms in GFF format from IsoSeq collapse.
- Several reference input files required across all steps of the pigeon workflow are described here.
The CLI workflow is described here.
The latest version of
pigeon is distributed through BioConda.
Version 0.1.0: Full changelog here