make.contigs for dual-index with heterogeneity spacers?

Commands in mothur
1

Hi,

I was just wondering if make.contigs with oligos option supports dual-index with heterogeneity spacer as described in https://microbiomejournal.biomedcentral.com/articles/10.1186/2049-2618-2-6#MOESM1?

I got raw pair-end fastq reads back from sequencing provider (one file each for R1 and R2) as they cannot demultiplex dual-index with heterogeneity spacer. I ran make.contigs with dual-index which seems to have worked but just want to make sure this is supported in mothur.

First few lines of my oligo file is as below:

primer GTGYCAGCMGCCGCGGTAA GGACTACNVGGGTWTCTAAT V3
barcode CCTAAACTACGG CCTAAACTACGG A
barcode TGCAGATCCAAC TGCAGATCCAAC B
barcode CCATCACATAGG CCATCACATAGG C
barcode GTGGTATGGGAGT GTGGTATGGGAGA D
barcode ACTTTAAGGGTGT ACTTTAAGGGTGA E
barcode GAGCAACATCCTT GAGCAACATCCTA F
barcode TGTTGCGTTTCTGT TGTTGCGTTTCTTC G
barcode ATGTCCGACCAAGT ATGTCCGACCAATC H
barcode AGGTACGCAATTGT AGGTACGCAATTTC I
barcode ACAGCCACCCATCGA ACAGCCACCCATCTA J

Thanks!

2

Yes, that should work. We tried this as we were developing the method in Kozich and found that we actually got a higher error rate than doing it by our approach.

Pat