Adapter, Primer removal

Hi everyone,

Could you please confirm whether the steps outlined in the MIseq SOP of mothur include the removal of adapters and primers sequences from raw reads? If so, could you also specify which command should be used for this purpose?

Thank You

Our wet lab SOP generates sequences without primers and index sequences so that isn’t explicitly included in the MiSeq SOP. If your approach retains the primers and indices, then you can give an oligos file to make.contigs. Alternatively, you can use trim.seqs to remove them after assembling the reads.


Thank You sir for your reply. I will try these two commands.
If I were to remove primers and adapters using a different tool and then proceed to process my reads using make.contigs , would this approach still be effective?

I strongly discourage using other tools to remove barcodes/primers/trim sequences. Pre-trimming results in poor sequence quality in our hands.


OK sir, Thank you for your valuable feedback.


make.contigs and trim.seqs have the option to remove primers and barcodes but don’t have option to remove adapters. How to remove adapters from raw reads?

How would you have the adapters on the sequences? I don’t think those get sequenced via Illumina. You might try playing with the linker and spacer sequence or add the adapter sequence to the barcode sequence