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