Find out which adaptors/barcodes were used in an illumina library?

[Genomics101]

I have a bunch of Illimina MiSeq sequences that look like they might have some adaptor/barcode contamination. I'd like to do some adaptor trimming but need to know which set were used in the sequencing. Does anyone know how to figure this out just from the data in the FASTQ files?

[kmcarr]

When you say adapter/barcode contamination do you mean that there were library fragments shorter than the read length so that there was read through into the adapter at the 3' end of the read?

You don't need to know the specific barcodes used used to effectively trim these, only the universal part of the adapter which is the part immediately adjacent to the 3' end if the insert. Trimmomatic includes standard adapter files for TruSeq and Nextera adapters. If the libraries were prepared with a third party kit it is likely the TruSeq adapter file would still work; most third party vendors do not redesign this part of the adapter since that would mean having to supply custom sequencing & index primers in order to sequence their libraries.

[Brian Bushnell]

I have a tool that finds the best overlap between two reads. This can be used for assembly (merging the reads into a single read) or adapter trimming; for example:

bbduk.sh -Xmx1g in1=r1.fq in2=r2.fq out1=trimmed1.fq out2=trimmed2.fq tbo ktrim=r

...will trim adapters of paired fragment libraries even if you don't know the adapter sequence. I have been meaning to automate the process of discovering and printing out unknown adapter sequences, but for now they just get trimmed. But you can identify them manually using BBMerge, with some effort. Or just assume TruSeq/Nextera as kmcarr mentioned, and use those (BBDuk will accept adapter files as well as trimming by overlap).