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 Nanopolish (version 0.10.2) to 

  • Detect SNPs and indels with respect to a reference genome.

App Creator

Amanda Cooksey

Quick Start

  • Nanopolish 0.10.2 variants takes the following files as input: 
  • Oxford Nanopore reads in FASTA format 
  • Corresponding FAST5 files
  • Indexed, sorted BAM file of those reads aligned to a reference genome 
  • Reference genome in FASTA format

Test Data


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

Input File(s)

Use these files from the folder above as example data:

raw_fast5_subset (FAST5 directory)


Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the section below.

Window: NC_016845.1:1-5333942

Ploidy: 1

Minimum candidate depth: 2

Leave all other parameters as default.

Output File(s)

With the above parameters Nanopolish variants creates one output file called variants_output.vcf.

Tool Source for App

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