RWilton

The error indicates that `srcId="1"` was specified in the AriocE configuration file for the encoded reads whereas `srcId="0"` was specified where those encoded reads were referenced in the AriocP configuration...

Ok. It's good that you have resolved this problem. Part of short-read DNA alignment folklore is that end-to-end alignment is superior in some way to soft-clipped alignment. This notion may...

I agree that your pipeline is unusual. Each of the recent problems you have reported have stemmed from the use of very short reference sequences and very short reads. These...