I used Mothur to trim a set of 454 sequences (used min and max length, qaverage=25, maxambig=0). I also used the Chimera Slayer and filter.seqs (on Mothur). I then imported a subset of these sequences into QIIME (I wanted to build some bootstrapped trees). I’ve noticed that the default trimming in QIIME includes removing any homopolymers >6 bp in length. I’m just wondering if anyone’s found that necessary, since I already cleaned up my files using the qual values on Mothur (and this additional step in Qiime is eliminating another ~3000 sequences from my already trimmed data set).
If anyone’s got insight into whether eliminating homopolymers is necessary, I’d appreciate it. I’ve looked at a couple articles, but haven’t really found what I’m looking for.