Query about Fastq quality filtering

[discoveradnan]

Hello everyone!!

At the end of Paired end sequencing run from illumina and generation of FASTQ files. Do we need to do quality trimming/filtering by third-party softwares or its already been taken care by Illumina fastQ generation pipeline?

Thanks

[GenoMax]

Even if it is (e.g. if the data was processed on MiSeq reporter/BaseSpace and the right boxes were checked) it would not hurt to pass the data through a scan/trim program.

If there no contaminants (adapters etc) there reads should come through unchanged, but if there are some remnants, they would be taken care of by the trim program.