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finder website  

finder is a gene annotator pipeline which automates the process of downloading short reads, aligning them and using the assembled transcripts to generate gene annotations. Additionally it uses protein sequences and reports gene predictions by BRAKER2. It is a fast, scalable, platform independent software that generatess gene annotations in GTF format. finder accepts inputs through command line interface. It finds several novel genes/transcripts and also reports the tissue/conditions they were found to be in.

Environment Modules

Run module spider finder to find out what environment modules are available for this application.

System Variables

  • HPC_FINDER_DIR - installation directory
  • HPC_FINDER_BIN - executable directory


If you publish research that uses finder you have to cite it as follows:

Sagnik Banerjee, Priyanka Bhandary, Margaret Woodhouse, Taner Z Sen,Roger P Wise, and Carson M Andorf. FINDER: An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences.bioRxiv, page 2021.02.04.429837, 2 2021.