mothur SOP Miseq: quality trimming


In the SOP Miseq decribed in Mothur website “examples”
I did no see how to make a quality trimming (Q25, or Q30) on the assembled sequence like it done using 454 data.
The results of make.contigs did not provide a file.qual (just the file.fasta), is there any reason for that??
thanks for help


I’ve been using trimmomatic on my Illumina data before starting mothur analyses. There are plenty of other options too.

The problem is that there is no straightforward way to make a consensus quality score for a base. If someone can point us to documentation on how this should be done, we’d gladly do it. E.g. imagine 2 sequence have different base calls in the same position of the contig. What should the quality score be? imagine they’re the same, what should the quality score be?

RDP just published a new paper for updating. It seems they improved PANDAseq, and integrate paird-ends Illumina assembler into RDPpipeline. They use some statistic model to calculate the overlapped bases score. The relevant part is called ‘Assembler for paired-end reads’, and more details is in supplementary document. Here is the link of this article:

I was wondering will mothur consider to use integrate other assembler or improve the current assembler for paired-end MiSeq sequencing data?


we’ll take a look at it - thanks for bringing it to our attention.