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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


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