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 

  • Extract FASTA or FASTQ files from FAST5 files.
  • This app should be run if your data were basecalled with Albacore 1.2 or earlier. If your data were basecalled with Albacore 2.0 or later you should use Nanopolish_index instead.

App Creator

Amanda Cooksey

Quick Start

  • Nanopolish 0.10.2 takes one or more FAST5 files or a folder of FAST5 files as input. 

Test Data


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

Input File(s)

Use the LomanLabz_PC_Ecoli_K12_R7.3_2549_1_ch8_file30_strand.fast5 files from the nanopolish directory for an example run. 

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)

Nanopolish extract will produce one or more FASTA or FASTQ files. Extraction of the example data as indicated above produces one FASTA file.

Tool Source for App

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