mothur

General question about make.contigs


#1

General question about make.contigs: What happens with paired reads that don’t overlap? In other words, if amplicon is longer than sum of paired reads, what will make.contigs do with those sequences?
Thanks!
Giovanni


#2

They will get assembled so that they overlap by a single base or the two reads will get assembled so that they full overlap. You can then remove such sequences by not allowing contigs over a certain length or those that contain ambiguous base calls.