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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Nanoqc - 0.9.1

This App runs nanoqc (version 0.9.1) to:

  • Provide quality control tools for long read sequencing data aiming to replicate some of the plots made by fastQC.
  • Creates dynamic plots using bokeh

App Creator

Alyssa Cochran

Quick Start

  • nanoqc 0.9.1 takes one fastq file 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 -> nanoqc 0.9.1

Input File(s)

Use the LomanLabz_PC_Ecoli_K12_R7.3_2549_1_ch8_file30_strand.fq 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)

nanoqc 0.9.1 will output a nanoQC.log and a nanoQC.html. nanoQC.html will show your plots in a web browser.

Tool Source for App

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