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 0.7.1) to 

  • Align signal-level events to k-mers of a reference genome.

App Creator

Amanda Cooksey

Quick Start

  • Nanopolish 0.7.1 eventalign takes the following files as input: 
  • Oxford Nanopore reads in FASTA format I
  • 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 -> eventalign -> version_0.7.1

Input File(s)

Use these files from the folder above as example data:

Reads file: 2258_subset.fa

 FAST5 folder: 

BAM alignment file: bwa_2258.bam

BAM index file: bwa_2258.bam.bai

Reference genome: Escherichia_coli_str._K-12_substr._MG1655_complete_genome.fasta


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.

Leave all parameters as default.

Output File(s)

With the above parameters Nanopolish eventalign creates one tab-separated output file called 'output.txt' 

Tool Source for App

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