Hi, i'm working with 3 samples of fungi, so i have ITS DNA sequences, reads are 151 bp long and Shotgun DNA sequencing (not amplification with primers) was performed by an external facility.
In my code i have demultiplexed them using demux-paired-end.
My question is the following: considering that during the shotgun sequencing, primers are not used, the step of Trimming sequence with cutadapt is needed or should i prosegue directly with the Denoising phase?
Is it required to do some other steps before the Denoising procedure ?
Thanks,
Francesco
Welcome in the forum!
If you dealing with fragment libraries I suggest to look at the Moshpit tutorial.
This is a qiime distribution fully oriented to process fragment libraries!
On your specific question, I would still use cutadapt to exclude sequencing primer sequences,
you probably need to ask to your facility which Illumina primer they used!
After that, you can work with Moshpit to taxonomy assign your sequences.