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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Nanopolish-index-0.10.2

This App runs Nanopolish (version 0.10.2) to 

  • Build an index mapping from basecalled reads to the signals measured by the sequencer.
  • This app should be run if your data were basecalled with Albacore 2.0 or later. If your data were basecalled with Albacore 1.2 or earlier you should use Nanopolish_extract instead.

App Creator

Amanda Cooksey

Quick Start

  • Nanopolish 0.10.2 takes a directory FAST5 files and basecalled reads in FASTA or FASTQ format as input. 

Test Data

Icon

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

Input File(s)

Use the the following files from the Nanopolish index directory above for an example run:

fast5_files directory

reads.fa 

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 index will produce the following files:

reads.fa.index

reads.fa.indexfai

reads.fa.index.gzi

reads.fa.index.readdb

Tool Source for App

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