Does the make.contigs command generate chimeras?

Hi all,

I would like to analyse my paired end Illumina data using mothur and starting from the r1 and r2 fastq files. The first step would be to use the make.contigs command and I want to better understand how it works.

Does the make.contigs command merge the forward and reverse reads based on the position of the DNA molecule on the flowcell, or does it try to merge sequences based on sequence similarity and by that increasing the change of forming chimeras?

All best,

It does it by aligning the sequences based on the flow cell position - your two fastq files should have the same number of reads with one file representing the forward and the other the reverse sequence for each spot on the flow cell. From there we align the reads. The method is described at