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  • reference genome in fasta format (may be gzipped) or an index (.mmi) of the reference genome
  • long reads in fastq or fasta format (may be gzipped)

Test Data


Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> minimap2


  • index.mmi
    • This is the index file of the genome generated by the app. This file may be used in future analyses in place of the reference genome fasta file.
  • output 
    • This is the alignment file generated by the app. It is in PAF format.  

Tool Source for App