Python tool that generates quality control statistics from FastQ file. A tool that accomplishes this task in the language R can be found [here] (https://github.com/dspak/CBB752_Final_Project_1.2). This tool is part of a set of bioinformatic and biological structure tools created for CBB752 at Yale University in the Spring 2016. The website containing the set of tools can be found [here] (http://cbb752spring2016.github.io).
The tool is named qualitystats.py. It takes one required input (name of the fastq file to be processed) and one optional input (the name of the txt file to which the filename and titles of the corresponding plots are output). This tool creates png files of the following plots:
-
Distribution of Read Lengths
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Per base quality score containing the median, quartiles, mean, and standard deviation
-
Distribution of mean quality per sequence
# Usage from terminal:
python3 qualitystats.py -i sample-input.fastq -o sample-output.txt
python3 qualitystats.py -i sample-input.fastq
Input Formats:
- input (-i): string of corresponding fastq file
- output (-o): string containing the name of the file to which the output information is saved
Output Format: txt file containing the file name, the number of sequences and the titles of corresponding plots
Quality Score Statistics and Figure names for sample-input.fastq
Number of Sequences = 100000
For the Distribution of read lengths see: Sequence_Length_Distribution.png
For a plot of the per base quality score see: Per_Base_Sequence_Quality.png
For a plot of the distribution of mean quality per sequence see: Per_Sequence_Mean_Quality_Distribution.png
