Advice for trimming asymmetric adapters for paired end sequencing library

Question

[song.michael12]

I was wondering if anyone had advice for the best software/commands to trim a paired-end sequencing library where the sequences are flanked with a pair of asymmetric adapters.

So basically we have a library of 300-1000 bp fragments, then we use Y-shaped adapters to ligate adapter sequence A to one end of the fragments, and adapter sequence B to the other end of the fragments. Then we throw Illumina TruSeq adapters onto both ends and perform paired-end sequencing on the library:

So our sequencing reads would look something like this:

5'-Adapter A-library fragment-Adapter B-3'

OR

5'-Adapter B-library fragment-Adapter A-3'

I thought about using cutadapt but I don't think it can be customized to the point of filtering reads with the logic (5' Adapter A AND 3' Adapter B) OR (5' Adapter B AND 3' Adapter A), or am I mistaken?

I was also considering performing the trimming operations sequentially, i.e. process case 1 (5' Adapter A AND 3' Adapter B), then process case 2 (5' Adapter B AND 3' Adapter A) in a separate operation. Would that be a more practical approach? Thanks in advance for any advice.

[h.mon]

Let me see if I understood this correctly: the output of the sequencing run will be either adapter A or adapter B, then the insert (library fragment), then either adapter A or B again, then Illumina Truseq adapter. Is this right? If so, you will have a combination of adapter(A|B)+Truseq adapters on the left side of the reads, and adapter(A|B) on the right side of the reads.

Are adapters A and B the same length? If so, you can right-trim a fixed number of bases, and left trim a custom combination of your adapters + Truseq adapters.

Answer 1

[Dattatray Mongad]

You can use trimmomatic for this kind of trimming where you can include your adapters in their adapter library and perform trimming.