NotSoFastQC 1.1

A tool to generate FastQC-like graphs from a FastQC file

NotSoFastQC

This package is designed to generate imitation reports for each module in the FastQC tool. All modules create filter text and QC report text files and selected modules generate graphs that mimic those seen in FastQC.

Installation

NotSoFastQC can be installed from my github repository, either by following the link or using git:

git clone https://github.com/jamesfox96/NotSoFastQC
cd NotSoFastQC
python setup.py install

Usage

NotSoFastQC can be run from the command line in a variety of ways based on your needs.

To run report generation for all modules:

NotSoFastQC -I fastqc.txt -O output_directory/ --all

OR

By manually selecting desired modules:

NotSoFastQC -I fastqc.txt -O output_directory/ -M 1 2 3 9 10 11

Options:

• -I: Input FastQC report text file.
• -O: Output directory.
• -D: To overwrite any folders in selected output directory with the same name as the folders generated.
• -M: To select individual module numbers separated by spaces.

OR

• --all: To select all modules for report generation. This will override any individually selected modules.

Details of modules available for selection are seen here below:

Module arg	Description
1	Per base sequence quality
2	Per tile sequence quality
3	Per sequence quality scores
4	Per base sequence content
5	Per sequence GC content
6	Per base N content
7	Sequence Length Distribution
8	Sequence Duplication Levels
9	Overrepresented sequences
10	Adapter Content
11	K-mer Content

Note: Module 11 (K-mer content) does not produce a FastQC-like graph. This is because of missing data in the given files

Rationale

NotSoFastQC has been created as part of an assignment submission for the Applied Bioinformatics module Introduction to Bioinformatics Using Python at Cranfield University. The package is designed to use the files supplied in the TestData/ folder.

Contact

James Fox: [e-mail]