Are adapter sequences trimmed from ONLY the 3' ends of reads

Question

[Pei]

Hello everyone!

I learn from this post[1] that Libraries prepared with Illumina library prep kits require adapter trimming only on the 3’ ends of reads, because adapter sequences are not found on the 5’ ends.

However, when we use tools like cutadapt, options are available for removing sequence of an adapter ligated to the 5' end of first or second mate.

It looked confusing to me. Did I make some misunderstanding on this issue?

My guess is that sequencing can also start from the adapter before the first base of the DNA insert in Reads 1 and 2. Am I right?

Thanks!

[1] https://support.illumina.com/bulletins/2016/04/adapter-trimming-why-are-adapter-sequences-trimmed-from-only-the--ends-of-reads.html

Answer 1

[Istvan Albert]

The options for 5' trimming are available because sometimes there may be additional adapters ligated there.

The regular 5' Illumina sequencing adapter is recognized and automatically trimmed by the instrument itself.

[GenoMax]

Actually sequencing primer is designed in such a way that the first base sequenced starts with base 1 of insert. There is an explanation of adapters in this document from Tufts Sequencing core.

[Pei]

Thanks Istvan and GenoMax!