Best Fastq Quality Overview Tool

Question

[William]

What is the best tool to get an overview of the quality of your produced reads (in a fastq file)?

FastQc http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ is sort of what I am looking for except that I want a PDF as output.

I want to run the tool as part of a pipeline on big files, so fast speed , memory efficient and multithreading is also important.

I know that I can convert the html to pdf but I thought that there would be alternative tools that give me a nice pdf immediatly.

This saves me having to convert the HTML to PDF and then delete all the html stuff.

Answer 1

[Irsan]

You can convert all the html images from FastQC to pdf with wkhtmltopdf with a single command:

wkhtmltopdf FastQCreport.html FastQCreport.pdf

Answer 2

[Pierre Lindenbaum]

FastQc http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ is sort of what I am looking for except that I want a PDF as output.

see

fastQC html report to PDF (with a script)