Quality check with barcordes

[agatharosa]

Hello guys!
I'm really beginner at bioinformatics.
I work with viral metagenomics and my library is going to be constructed with Nextera XT for Illumina sequencing. Double barcodes will be used for each pool.
I'm thinking how can I do the quality check of my reads if I have barcodes to identify them. I will use NGSTollkit to make this, but, as I realize, It is impossible to use the Trimming tool because the barcodes needs to stay entire. Is just the QC tool enough?

The best,

Agatha.

[GenoMax]

In Illumina sequencing the index/barcode reads are never part of the actual read so you don't ever need to worry about those being affected by trimming.

For QC checking, FastQC is what most people use: http://www.bioinformatics.babraham.a...ojects/fastqc/

For trimming you can use trimmomatic, bbduk.sh, cutadapt. You will find individual threads for these tools here.