I have some metagenomics reads, I trim them with trimmomatic and remove adapters using some illumina adapters library I found on the internet.
Then I look at them in Fastqc and it says that "adapter content" is very bad and "kmer content" is very bad as well (which must mean that there are indeed lots of adapters), the question is -- how do I remove these adapters?
How does Fastqc know they are there? Is it using some adapter database? If so, I would like to use that database to remove them! Where is the Fullest Possible Illumina Adapters Library (because the one I'm using right now isn't full enough)? Or Fastqc is mistaking?