The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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This App runs Minimap2 (version 2.10) to:

find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome.

App Creator

Amanda Cooksey

Quick Start

Minimap2 requires the following:
  • 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


Input File(s)

  • Reference genome fasta file
    • GCF_000146045.2_R64_genomic.fna.gz
  • Oxford Nanopore reads file
    • SRR6059712.fastq

Parameters Used in App

  • In the Index Parameters section choose the reference genome fasta input file: 'GCF_000146045.2_R64_genomic.fna.gz'.
  • In the Index Parameters section enter a file name (index.mmi) in the 'Dump index to FILE' field to save the index file created by the app.
  • In the Mapping and Alignment section select the Oxford Nanopore reads input file: 'SRR6059712.fastq'. 
  • In the Mapping and Alignment section select 'long-read spliced alignment' from the 'preset options' drop-down menu.
  • All remaining parameters may be left as default. 

Output File(s)

  • 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

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