Hi, I’ve been using make.contigs (with a 4-column oligos file) in our pipeline for a while. I understand it has a lot of bells and whistles under the hood. Demultiplexing, removing primers, pair merging, etc.
I now have 2 questions.
Our reads are longer than the amplicons. Therefore, R1 will extend into the reverse primer, and R2 will extend into the forward primer. Is there a clean way to handle this within make.contigs ? Right now, I have to call upon cutadapt on the merged reads out of make.contigs to remove those read-through primers
What exactly are the quality filtering parameters we can use/set within make.contigs? Insert, deltaq, maxee ?
The maxee is the same as that’s used with Vsearch ? does it have a default value in make.contigs ?
Do we have an option to set the minimum overlap length (as the -v parameter in PEAR) ?
The insert, is it the same as the -q parameter in PEAR (quality score threshold for
trimming the low-quality reads) ?