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Supported Tool

A tool to compare, merge and annotate one or more GFF files with a reference annotation in GFF format.


The program gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the “query” files), when compared with a reference annotation (also provided as GFF).

The Sensitivity / Precision values are displayed in a single plot, different loci levels can be switched by choosing a different dataset.


Please use gffcompare only with single samples. Multi-Sample comparisons are not correctly rendered by this MultiQC module.

Note that exported data in multiqc_data/multiqc_gffcompare.{tsv,yaml,json} only works when exporting with YAML or JSON - the default .tsv output will not contain any data. Please use -k yaml or -k json to export in a structured format. It is hoped to refactor this code in a future release - please submit a PR if you are interested.

File search patterns

  fn: "*.stats"
  contents: "# gffcompare"
  num_lines: 2