What Quality Control software should i use?

Question

[bondcarbond]

Hi all,

I want to performe a quality control for illumina sequenced data and i found several softwares (FASTQC, FASTQCs, HTQC, prinseq, htseq-qa) that coud performe this task. I wanted to ask if anyone with expierence could recommend me one in specific.

tahnks for the help!

[venu]

Did you check this Fastq Quality Control Shootout

Answer 1

[thackl]

I'd recommend FASTQC. It's fast, easy to use and comprehensive.

[Brian Bushnell]

I like FastQC's plots, but my impression of it was as a quality-analysis/visualization tool that does not actually change the input (please correct me if I'm wrong). For actually addressing issues present in data, you need to use a different too that can trim and filter the reads, such as BBDuk.

As an alternative to FastQC, you might also look at fastqp, mentioned here: FastQC quality control graphics for publication?