The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

The box below searches only this space.
To search the entire iPlant wiki, enter your query in the box at the upper right.

 

 

 

 

 

Skip to end of metadata
Go to start of metadata

FastQC-plus 0.10.1 (multi-file)

FastQC-plus aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. This version runs the application on multiple files and creates a summary output page for all files in .html format. 

Quick Start

NOTE: FastQC will determine the format that your FASTQ reads are in (PHRED33, Illumina, etc). The detected read type will be listed on the graphs outputted. As an additional note, PHRED33 is exactly the same as Solexa / Illumina 1.9, thus if using these FASTQ files in downstream apps such as the FASTX toolkit, you will need to select PHRED33 for your format type if your reads are in Solexa/Illumina 1.9 format.

Test Data

Community Data > iplantcollaborative > example_data > fastqc_plus > inputs 

Input File(s): 

ATreads.fq and ATreads2.fq

fastq files 

Parameters Used in App

No parameters 

Output File(s)

fastqc_summary.html contains a summarized report for all entries. Original FastQC outputs placed in the intermediate_files directory.

Community Data > iplantcollaborative > example_data > fastqc_plus > output2 

Tool Source for App