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.