Using just forward primers in mothur


I’m trying to regenerate the archaeal communities (primer: Arch349f-806r) using mothur (we used QIIME2 before), and it seems that the reverse reads have very bad qualities so the remove.seqs after alignment remove all the sequences. Therefore, we would like to just use forward reads for the mothur pipeline. Those sequences are generated from Miseq and are demultiplexed. How can I merge just the forward sequences to enable it for the downstream analysis?


Hi - you could use to separate the quality scores and fasta data and then run it through trim.seqs to quality/length trim your single read sequences