How to detect unknown primer sequence

Question

[genetixs]

Hello, for a project I have, the fungi samples sequenced with iseq 1000 are available in fastq format, but I do not have the primer sequence and adapter sequence information used in this run. Kit Swift 16S+ITS panel used. How can I remove the primer sequence from these fungi sample?

Answer 1

[Buffo]

You can check first what the quality looks like, and check whether there is any contamination in your fastq files with fastqc. Then you can use Trimmomatic to trim adapters (if any) using the ILLUMINACLIP command. Read the manual, trimmomatic has a list of Illumina adapters ready to be used.

Answer 2

[GenoMax]

The question is about a specific kit from Swift biosciences. Swift was acquired by IDT in last couple of years. It looks like primer and adapter sequences are available from IDT here (Check application note and then look in appendix here)