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Advice for trimming asymmetric adapters for paired end sequencing library
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2.2 years ago

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'


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.

sequencing • 489 views
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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.

Entering edit mode
19 months ago
National Centre for Cell Science, Pune

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


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