This repository has been marked as deprecated, so some tool shed features may be restricted.
Repository 'fastqc'
http://toolshed.g2.bx.psu.edu/view/jjohnson/fastqc
fastqc
unrestricted
quality control checks on raw sequence data
FastQC ( http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ )
performs quality control checks on raw sequence data (FASTQ, SAM, BAM) 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. 
0:1d373f219445
jjohnson
True
204

Repository README files - may contain important installation or license information


FastQC
------

From the FastQC website   http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

Function A quality control tool for high throughput sequence data.
Language Java
Requirements A suitable Java Runtime Environment 
The Picard BAM/SAM Libraries (included in download)
Code Maturity Stable. Mature code, but feedback is appreciated.
Code Released Yes, under GPL v3 or later.
Initial Contact Simon Andrews

FastQC 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.

The main functions of FastQC are:

- Import of data from BAM, SAM or FastQ files (any variant)
- Providing a quick overview to tell you in which areas there may be problems
- Summary graphs and tables to quickly assess your data
- Export of results to an HTML based permanent report
- Offline operation to allow automated generation of reports without running the interactive application

Download and installation information is at: http://www.bioinformatics.bbsrc.ac.uk/projects/download.html#fastqc


Galaxy Tool Wrapper
-------------------

The galaxy tool wrapper for FastQC requires version:   FastQC v0.7.2 

FastQC should be downloaded and installed on the system on which it will be executed.  
The PATH environment variable should include the directory in which the fastqc script resides.

The fastqc.py wrapper invokes the fastqc script provided in FastQC download, 
and converts the FastQC results into a Galaxy html formatted dataset.


Contents of this repository

Name Description Version
FastQC quality control checks on raw sequence data 1.0.0

Automated tool test results

Time tested: 2014-04-22 15:12:44
System:
Architecture:
Python version:
Galaxy revision:
Galaxy database version:
Tool shed revision: 13123:e6876f691854
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: FastQC
Tool version: 1.0.0
Tool guid: toolshed.g2.bx.psu.edu/repos/jjohnson/fastqc/FastQC/1.0.0
Missing components:
Repository does not have a test-data directory. Functional test definitions missing for FastQC.

Categories
Fasta Manipulation
Sequence Analysis

Rating
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