A general question; Illumina has launched the new platforms and they are providing binned q scores (every five bases) instead of the base by base. I was wondering if there is a planned update to be able to run those samples in mothur. Although, to be honest, I am not sure I would like to run my samples in those platforms if quality scores will be binned and one cannot really know how clean it was.
Interesting. I had not heard this. If you or anyone have any mock community data, I’d be happy to take a look. My sense is that make.contigs
should perform about the same as it had before. Our deltaQ value is 6, and as I recall the difference between 5 and 6 was pretty minimal.
Pat