FraserQC

A quality control tool for high throughput sequence data

fraserQC.py

Data quality control and data statistics for high throughput sequences

Usage: python fraserQC.py [options] -i fastqFile -s sampleName -o outputFolder

Options:

--version                               show program's version number and exit
-h, --help                              show this help message and exit
-s SAMPLENAME, --sampleName=SAMPLENAME  [REQUIRED] sample name for fastq files
-i FQLIST, --fqList=FQLIST              [REQUIRED] input fastq files ended with fq/fastq/gz (PEs were separated by ",")
-o FOLDER, --outputFolder=FOLDER        [REQUIRED] In this folder, the program will create sample-specific folder, containning all qc result 
-f, --filter                            perform quality trim by htqc [default to skip this step]
-m, --watermarker                       print out water marker [default to not print water marker]

Advanced Options:

-w INT              window size for quality trim [default: 5]
-C INT              quality threshold for trim [default: 20]
-L INT              length threshold for trim [default: 50]

Example: python fraserQC.py -f -L 100 -C 30 -w 10 -i test_1.fq.gz,test_2.fq.gz -t 2 -s test -o outdir

Dependencies:

• FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
• htqc (https://sourceforge.net/projects/htqc/)
• R

How to use this tool:

1. Install FastQC, htqc and R
2. Modify fraserQC.py with the install path of FastQC and htqc. Specifically modify the script at line 417 and 421