sffinfo trimming 1 extra good base


I’m using sffinfo within mothur as follows:

mothur -q “#sffinfo(sff=454Reads.RL6.sff, flow=F);”

I get the FASTA & QUAL files as expected. What I’ve noticed is that an extra base ( one more than what is indicated in “Clip Qual Right:” ) is trimmed off. Looks like it may be an off-by-one bug here. A visual look at the soft masked bases within the SFF file can confirm this as well.

With regards to “Clip Qual Right:” , this is not how sffinfo from 454tools or process_sff.py from QIIME is functioning during SFF to FASTA conversion.

Can you confirm this behavior on your end? Am I missing something obvious? I will admit I’m a new user to mothur and how SFF files are processed.

Let me know if you require me to provide some examples.

Thanks for your support on this.


I wanted to add that I’m using version:

mothur v.1.35.1
Last updated: 03/31/2015

Another question: does sffinfo always read ‘Clip Qual Left:’ to be 5 ?



Thanks for reporting this bug Mike. I have fixed the issue and the change will be part of our next release 1.36.0.